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Sample records for short test sequence

  1. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  2. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  3. BLEACHING EUCALYPTUS PULPS WITH SHORT SEQUENCES

    Directory of Open Access Journals (Sweden)

    Flaviana Reis Milagres

    2011-03-01

    Full Text Available Eucalyptus spp kraft pulp, due to its high content of hexenuronic acids, is quite easy to bleach. Therefore, investigations have been made attempting to decrease the number of stages in the bleaching process in order to minimize capital costs. This study focused on the evaluation of short ECF (Elemental Chlorine Free and TCF (Totally Chlorine Free sequences for bleaching oxygen delignified Eucalyptus spp kraft pulp to 90% ISO brightness: PMoDP (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, PMoD/P (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, without washing PMoD(PO (Molybdenum catalyzed acid peroxide, chlorine dioxide and pressurized peroxide, D(EPODP (chlorine dioxide, extraction oxidative with oxygen and peroxide, chlorine dioxide and hydrogen peroxide, PMoQ(PO (Molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide, and XPMoQ(PO (Enzyme, molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide. Uncommon pulp treatments, such as molybdenum catalyzed acid peroxide (PMo and xylanase (X bleaching stages, were used. Among the ECF alternatives, the two-stage PMoD/P sequence proved highly cost-effective without affecting pulp quality in relation to the traditional D(EPODP sequence and produced better quality effluent in relation to the reference. However, a four stage sequence, XPMoQ(PO, was required to achieve full brightness using the TCF technology. This sequence was highly cost-effective although it only produced pulp of acceptable quality.

  4. Optimization of short amino acid sequences classifier

    Science.gov (United States)

    Barcz, Aleksy; Szymański, Zbigniew

    This article describes processing methods used for short amino acid sequences classification. The data processed are 9-symbols string representations of amino acid sequences, divided into 49 data sets - each one containing samples labeled as reacting or not with given enzyme. The goal of the classification is to determine for a single enzyme, whether an amino acid sequence would react with it or not. Each data set is processed separately. Feature selection is performed to reduce the number of dimensions for each data set. The method used for feature selection consists of two phases. During the first phase, significant positions are selected using Classification and Regression Trees. Afterwards, symbols appearing at the selected positions are substituted with numeric values of amino acid properties taken from the AAindex database. In the second phase the new set of features is reduced using a correlation-based ranking formula and Gram-Schmidt orthogonalization. Finally, the preprocessed data is used for training LS-SVM classifiers. SPDE, an evolutionary algorithm, is used to obtain optimal hyperparameters for the LS-SVM classifier, such as error penalty parameter C and kernel-specific hyperparameters. A simple score penalty is used to adapt the SPDE algorithm to the task of selecting classifiers with best performance measures values.

  5. Short read sequence typing (SRST: multi-locus sequence types from short reads

    Directory of Open Access Journals (Sweden)

    Inouye Michael

    2012-07-01

    Full Text Available Abstract Background Multi-locus sequence typing (MLST has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel

  6. Short- circuit tests of circuit breakers

    OpenAIRE

    Chorovský, P.

    2015-01-01

    This paper deals with short-circuit tests of low voltage electrical devices. In the first part of this paper, there are described basic types of short- circuit tests and their principles. Direct and indirect (synthetic) tests with more details are described in the second part. Each test and principles are explained separately. Oscilogram is obtained from short-circuit tests of circuit breakers at laboratory. The aim of this research work is to propose a test circuit for performing indirect test.

  7. A short TE gradient-echo sequence using asymmetric sampling

    International Nuclear Information System (INIS)

    Fujita, Norihiko; Harada, Kohshi; Sakurai, Kosuke; Nakanishi, Katsuyuki; Kim, Shyogen; Kozuka, Takahiro

    1990-01-01

    We have developed a gradient-echo pulse sequence with a short TE less than 4 msec using a data set of asymmetric off-center sampling with a broad bandwidth. The use of such a short TE significantly reduces T 2 * dephasing effect even in a two-dimensional mode, and by collecting an off-center echo, motion-induced phase dispersion is also considerably decreased. High immunity of this sequence to these dephasing effects permits clear visualization of anatomical details near the skull base where large local field inhomogeneities and rapid blood flow such as in the internal carotid artery are present. (author)

  8. Studying a free fall experiment using short sequences of images

    International Nuclear Information System (INIS)

    Vera, Francisco; Romanque, Cristian

    2008-01-01

    We discuss a new alternative for obtaining position and time coordinates from a video of a free fall experiment. In our approach, after converting the video to a short sequence of images, the images are analyzed using a web page application developed by the author. The main advantage of the setup explained in this work, is that it is simple to use, no software license fees are necessary, and can be scaled-up to be used by a big number of students in introductory physics courses. The steps involved in the full analysis of a falling object are: we grab a short digital video of the experiment and convert it to a sequence of images, then, using a web page that includes all the necessary javascript, the student can easily click on the object of interest to obtain the (x,y,t) coordinates, finally, the student analyze motion using a spreadsheet.

  9. SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

    Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

  10. Short Note DNA sequences from the Little Brown Bustard Eupodotis ...

    African Journals Online (AJOL)

    Taxonomic classification of birds based exclusively on morphology and plumage traits has often been found to be inconsistent with true evolutionary history when tested with molecular phylogenies based on neutrally evolving markers. Here we present cytochrome-b gene sequences for the poorly known Little Brown ...

  11. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  12. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    Automated software testing aims to detect errors by producing test inputs that cover as much of the application source code as possible. Applications for mobile devices are typically event-driven, which raises the challenge of automatically producing event sequences that result in high coverage...

  13. Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

    DEFF Research Database (Denmark)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao

    2016-01-01

    developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels......Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

  14. A test matrix sequencer for research test facility automation

    Science.gov (United States)

    Mccartney, Timothy P.; Emery, Edward F.

    1990-01-01

    The hardware and software configuration of a Test Matrix Sequencer, a general purpose test matrix profiler that was developed for research test facility automation at the NASA Lewis Research Center, is described. The system provides set points to controllers and contact closures to data systems during the course of a test. The Test Matrix Sequencer consists of a microprocessor controlled system which is operated from a personal computer. The software program, which is the main element of the overall system is interactive and menu driven with pop-up windows and help screens. Analog and digital input/output channels can be controlled from a personal computer using the software program. The Test Matrix Sequencer provides more efficient use of aeronautics test facilities by automating repetitive tasks that were once done manually.

  15. LS1 Report: short-circuit tests

    CERN Multimedia

    Katarina Anthony

    2014-01-01

    As the LS1 draws to an end, teams move from installation projects to a phase of intense testing. Among these are the so-called 'short-circuit tests'. Currently under way at Point 7, these tests verify the cables, the interlocks, the energy extraction systems, the power converters that provide current to the superconducting magnets and the cooling system.   Thermal camera images taken during tests at point 4 (IP4). Before putting beam into the LHC, all of the machine's hardware components need to be put to the test. Out of these, the most complicated are the superconducting circuits, which have a myriad of different failure modes with interlock and control systems. While these will be tested at cold - during powering tests to be done in August - work can still be done beforehand. "While the circuits in the magnets themselves cannot be tested at warm, what we can do is verify the power converter and the circuits right up to the place the cables go into the magn...

  16. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  17. Irreducible Tests for Space Mission Sequencing Software

    Science.gov (United States)

    Ferguson, Lisa

    2012-01-01

    As missions extend further into space, the modeling and simulation of their every action and instruction becomes critical. The greater the distance between Earth and the spacecraft, the smaller the window for communication becomes. Therefore, through modeling and simulating the planned operations, the most efficient sequence of commands can be sent to the spacecraft. The Space Mission Sequencing Software is being developed as the next generation of sequencing software to ensure the most efficient communication to interplanetary and deep space mission spacecraft. Aside from efficiency, the software also checks to make sure that communication during a specified time is even possible, meaning that there is not a planet or moon preventing reception of a signal from Earth or that two opposing commands are being given simultaneously. In this way, the software not only models the proposed instructions to the spacecraft, but also validates the commands as well.To ensure that all spacecraft communications are sequenced properly, a timeline is used to structure the data. The created timelines are immutable and once data is as-signed to a timeline, it shall never be deleted nor renamed. This is to prevent the need for storing and filing the timelines for use by other programs. Several types of timelines can be created to accommodate different types of communications (activities, measurements, commands, states, events). Each of these timeline types requires specific parameters and all have options for additional parameters if needed. With so many combinations of parameters available, the robustness and stability of the software is a necessity. Therefore a baseline must be established to ensure the full functionality of the software and it is here where the irreducible tests come into use.

  18. Sequence robust association test for familial data.

    Science.gov (United States)

    Dai, Wei; Yang, Ming; Wang, Chaolong; Cai, Tianxi

    2017-09-01

    Genome-wide association studies (GWAS) and next generation sequencing studies (NGSS) are often performed in family studies to improve power in identifying genetic variants that are associated with clinical phenotypes. Efficient analysis of genome-wide studies with familial data is challenging due to the difficulty in modeling shared but unmeasured genetic and/or environmental factors that cause dependencies among family members. Existing genetic association testing procedures for family studies largely rely on generalized estimating equations (GEE) or linear mixed-effects (LME) models. These procedures may fail to properly control for type I errors when the imposed model assumptions fail. In this article, we propose the Sequence Robust Association Test (SRAT), a fully rank-based, flexible approach that tests for association between a set of genetic variants and an outcome, while accounting for within-family correlation and adjusting for covariates. Comparing to existing methods, SRAT has the advantages of allowing for unknown correlation structures and weaker assumptions about the outcome distribution. We provide theoretical justifications for SRAT and show that SRAT includes the well-known Wilcoxon rank sum test as a special case. Extensive simulation studies suggest that SRAT provides better protection against type I error rate inflation, and could be much more powerful for settings with skewed outcome distribution than existing methods. For illustration, we also apply SRAT to the familial data from the Framingham Heart Study and Offspring Study to examine the association between an inflammatory marker and a few sets of genetic variants. © 2017, The International Biometric Society.

  19. De novo assembly of human genomes with massively parallel short read sequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue

    2010-01-01

    genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities...... for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way....

  20. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

    NARCIS (Netherlands)

    Semenova, E.V.; Jore, M.M.; Westra, E.R.; Oost, van der J.; Brouns, S.J.J.

    2011-01-01

    Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)/Cas (CRISPR-associated sequences) systems provide adaptive immunity against viruses when a spacer sequence of small CRISPR RNA (crRNA) matches a protospacer sequence in the viral genome. Viruses that escape CRISPR/Cas

  1. ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

    Science.gov (United States)

    Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

    2014-02-01

    Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

  2. Car sequencing is NP-hard: a short proof

    OpenAIRE

    B Estellon; F Gardi

    2013-01-01

    In this note, a new proof is given that the car sequencing (CS) problem is NP-hard. Established from the Hamiltonian Path problem, the reduction is direct while closing some gaps remaining in the previous NP-hardness results. Since CS is studied in many operational research courses, this result and its proof are particularly interesting for teaching purposes.

  3. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences.

    Directory of Open Access Journals (Sweden)

    Mohammed Bakkali

    Full Text Available Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES causes preferential uptake of conspecific DNA, but the function(s behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein

  4. Accurate estimation of short read mapping quality for next-generation genome sequencing

    Science.gov (United States)

    Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

    2012-01-01

    Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

  5. Tools for analyzing genetic variants from sequencing data Case study: short tandem repeats

    OpenAIRE

    Gymrek, Melissa

    2016-01-01

    This was presented as a BitesizeBio Webinar entitled "Tools for analyzing genetic variants from sequencing data Case study: short tandem repeats"Accompanying scripts can be accessed on github:https://github.com/mgymrek/mgymrek-bitesizebio-webinar 

  6. Characterization of Campylobacter jejuni applying flaA short variable region sequencing, multilocus sequencing and Fourier transform infrared spectroscopy

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Bonnichsen, Lise; Larsson, Jonas

    flaA short variable region sequencing and phenetic Fourier transform infrared (FTIR) spectroscopy was applied on a collection of 102 Campylobacter jejuni isolated from continuous sampling of organic, free range geese and chickens. FTIR has been shown to serve as a valuable tool in typing...

  7. Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.

    Directory of Open Access Journals (Sweden)

    Arthur W Pightling

    Full Text Available The wide availability of whole-genome sequencing (WGS and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i depth of sequencing coverage, ii choice of reference-guided short-read sequence assembler, iii choice of reference genome, and iv whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT, using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming. We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers

  8. SRComp: short read sequence compression using burstsort and Elias omega coding.

    Directory of Open Access Journals (Sweden)

    Jeremy John Selva

    Full Text Available Next-generation sequencing (NGS technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain applications where compression time is of major concern.

  9. 3D reconstruction software comparison for short sequences

    Science.gov (United States)

    Strupczewski, Adam; Czupryński, BłaŻej

    2014-11-01

    Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

  10. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    DEFF Research Database (Denmark)

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas

    2014-01-01

    , a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred...... nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior...

  11. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

    DEFF Research Database (Denmark)

    Mourier, Tobias; Mollerup, Sarah; Vinner, Lasse

    2015-01-01

    From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs...... to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads...

  12. Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs.

    Science.gov (United States)

    Guarracino, Danielle A; Gentile, Kayla; Grossman, Alec; Li, Evan; Refai, Nader; Mohnot, Joy; King, Daniel

    2018-02-01

    Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3 10 -helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3 10 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

  13. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  14. Testing the Predictive Power of Coulomb Stress on Aftershock Sequences

    Science.gov (United States)

    Woessner, J.; Lombardi, A.; Werner, M. J.; Marzocchi, W.

    2009-12-01

    Empirical and statistical models of clustered seismicity are usually strongly stochastic and perceived to be uninformative in their forecasts, since only marginal distributions are used, such as the Omori-Utsu and Gutenberg-Richter laws. In contrast, so-called physics-based aftershock models, based on seismic rate changes calculated from Coulomb stress changes and rate-and-state friction, make more specific predictions: anisotropic stress shadows and multiplicative rate changes. We test the predictive power of models based on Coulomb stress changes against statistical models, including the popular Short Term Earthquake Probabilities and Epidemic-Type Aftershock Sequences models: We score and compare retrospective forecasts on the aftershock sequences of the 1992 Landers, USA, the 1997 Colfiorito, Italy, and the 2008 Selfoss, Iceland, earthquakes. To quantify predictability, we use likelihood-based metrics that test the consistency of the forecasts with the data, including modified and existing tests used in prospective forecast experiments within the Collaboratory for the Study of Earthquake Predictability (CSEP). Our results indicate that a statistical model performs best. Moreover, two Coulomb model classes seem unable to compete: Models based on deterministic Coulomb stress changes calculated from a given fault-slip model, and those based on fixed receiver faults. One model of Coulomb stress changes does perform well and sometimes outperforms the statistical models, but its predictive information is diluted, because of uncertainties included in the fault-slip model. Our results suggest that models based on Coulomb stress changes need to incorporate stochastic features that represent model and data uncertainty.

  15. Lead time reduction by optimal test sequencing

    NARCIS (Netherlands)

    Boumen, R.; Jong, de I.S.M.

    2005-01-01

    Het testen van machines neemt in het huidige ontwerp en productie fases binnen ASML ongeveer 30-50% van de totale doorlooptijd in. Om deze tijd te verkorten, worden er test strategieën gemaakt. Een van de belangrijke onderdelen van zo een test strategie is de test volgorde, oftewel de volgorde

  16. Testing for Short Memory in a VARMA Process

    OpenAIRE

    Oke, Timothy; Öller, Lars-Erik

    1997-01-01

    We generalize the short term memory test of an ARMA model, presented in Öller (1985), to the multivariate VARMA cases. In a study on Swedish exports and OECD demand we demonstrate how the multivariate setting extends the short memory.

  17. Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India.

    Directory of Open Access Journals (Sweden)

    Saroj K Young

    2008-04-01

    Full Text Available Inadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological studies and contribute to our understanding of the disease.Genotyping assays based on variation in the copy number of short tandem repeat sequences were applied to biopsies collected in population-based epidemiological studies of leprosy in northern Malawi, and from members of multi-case households in Hyderabad, India. In the Malawi series, considerable genotypic variability was observed between patients, and also within patients, when isolates were collected at different times or from different tissues. Less within-patient variability was observed when isolates were collected from similar tissues at the same time. Less genotypic variability was noted amongst the closely related Indian patients than in the Malawi series.Lineages of M. leprae undergo changes in their pattern of short tandem repeat sequences over time. Genetic divergence is particularly likely between bacilli inhabiting different (e.g., skin and nerve tissues. Such variability makes short tandem repeat sequences unsuitable as a general tool for population-based strain typing of M. leprae, or for distinguishing relapse from reinfection. Careful use of these markers may provide insights into the development of disease within individuals and for tracking of short transmission chains.

  18. HEURISTIC METHODS FOR TEST SEQUENCING IN TELECOMMUNICATION SATELLITES

    OpenAIRE

    Boche-Sauvan , Ludivine; Cabon , Bertrand; Huguet , Marie-José; Hébrard , Emmanuel

    2014-01-01

    Colloque avec actes et comité de lecture. internationale.; International audience; The increasing complexity in telecommunication satellite payload design demands new test sequencing approaches to face the induced increase of validation complexity. In such a sequencing problem, each test requires specific payload equipment states at a dedicated temperature range. The industrial objectives are both to reduce the total time of tests and to keep the thermal stability of the payload. For solving ...

  19. TMS Over the Cerebellum Interferes with Short-term Memory of Visual Sequences.

    Science.gov (United States)

    Ferrari, C; Cattaneo, Z; Oldrati, V; Casiraghi, L; Castelli, F; D'Angelo, E; Vecchi, T

    2018-04-30

    Growing evidence suggests that the cerebellum is not only involved in motor functions, but it significantly contributes to sensory and cognitive processing as well. In particular, it has been hypothesized that the cerebellum identifies recurrent serial events and recognizes their violations. Here we used transcranial magnetic stimulation (TMS) to shed light on the role of the cerebellum in short-term memory of visual sequences. In two experiments, we found that TMS over the right cerebellar hemisphere impaired participants' ability to recognize the correct order of appearance of geometrical stimuli varying in shape and/or size. In turn, cerebellar TMS did not affect recognition of highly familiar short sequences of letters or numbers. Overall, our data suggest that the cerebellum is involved in memorizing the order in which (concatenated) stimuli appear, this process being important for sequence learning.

  20. A sensitive short read homology search tool for paired-end read sequencing data.

    Science.gov (United States)

    Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

    2017-10-16

    Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

  1. Electrical short circuit and current overload tests on aircraft wiring

    Science.gov (United States)

    Cahill, Patricia

    1995-01-01

    The findings of electrical short circuit and current overload tests performed on commercial aircraft wiring are presented. A series of bench-scale tests were conducted to evaluate circuit breaker response to overcurrent and to determine if the wire showed any visible signs of thermal degradation due to overcurrent. Three types of wire used in commercial aircraft were evaluated: MIL-W-22759/34 (150 C rated), MIL-W-81381/12 (200 C rated), and BMS 1360 (260 C rated). A second series of tests evaluated circuit breaker response to short circuits and ticking faults. These tests were also meant to determine if the three test wires behaved differently under these conditions and if a short circuit or ticking fault could start a fire. It is concluded that circuit breakers provided reliable overcurrent protection. Circuit breakers may not protect wire from ticking faults but can protect wire from direct shorts. These tests indicated that the appearance of a wire subjected to a current that totally degrades the insulation looks identical to a wire subjected to a fire; however the 'fire exposed' conductor was more brittle than the conductor degraded by overcurrent. Preliminary testing indicates that direct short circuits are not likely to start a fire. Preliminary testing indicated that direct short circuits do not erode insulation and conductor to the extent that ticking faults did. Circuit breakers may not safeguard against the ignition of flammable materials by ticking faults. The flammability of materials near ticking faults is far more important than the rating of the wire insulation material.

  2. Sequence composition and gene content of the short arm of rye (Secale cereale chromosome 1.

    Directory of Open Access Journals (Sweden)

    Silvia Fluch

    Full Text Available BACKGROUND: The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3% being the most abundant. More than four thousand simple sequence repeat (SSR sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. CONCLUSIONS: The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.

  3. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

    Science.gov (United States)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W; Grassa, Christopher J; Geraldes, Armando; Cronk, Quentin C; Cullis, Christopher; Dash, Prasanta K; Kumar, Polumetla A; Cloutier, Sylvie; Sharpe, Andrew G; Wong, Gane K-S; Wang, Jun; Deyholos, Michael K

    2012-11-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  4. Correction of echo shift in reconstruction processing for ultra-short TE pulse sequence

    International Nuclear Information System (INIS)

    Takizawa, Masahiro; Ootsuka, Takehiro; Abe, Takayuki; Takahashi, Tetsuhiko

    2010-01-01

    An ultra-short echo time (TE) pulse sequence is composed of a radial sampling that acquires echo signals radially in the K-space and a half-echo acquisition that acquires only half of the echo signal. The shift in the position of the echo signal (echo shift) caused by the timing errors in the gradient magnetic field pulses affects the image quality in the radial sampling with the half-echo acquisition. To improve image quality, we have developed a signal correction algorithm that detects and eliminates this echo shift during reconstruction by performing a pre-scan within 10 seconds. The results showed that image quality is improved under oblique and/or off-centering conditions that frequently cause image distortion due to hardware error. In conclusion, we have developed a robust ultra-short TE pulse sequence that allows wide latitude in the scan parameters, including oblique and off-centering conditions. (author)

  5. SeqEntropy: genome-wide assessment of repeats for short read sequencing.

    Directory of Open Access Journals (Sweden)

    Hsueh-Ting Chu

    Full Text Available BACKGROUND: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free reads at different lengths. METHODOLOGY/PRINCIPAL FINDINGS: We define a metric H(k to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k. In our experiments, we found that entropy loss correlates well with de-novo assembly coverage of a genome, and a score of ΔH(k>1% indicates a severe loss in genome reconstruction fidelity. The minimal read lengths to achieve ΔH(k<1% are different for various organisms and are independent of the genome size. For example, in order to meet the threshold of ΔH(k<1%, a read length of 60 bp is needed for the sequencing of human genome (3.2 10(9 bp and 320 bp for the sequencing of fruit fly (1.8×10(8 bp. We also calculated the ΔH(k scores for 2725 prokaryotic chromosomes and plasmids at several read lengths. Our results indicate that the levels of repeats in different genomes are diverse and the entropy of sequencing reads provides a measurement for the repeat structures. CONCLUSIONS/SIGNIFICANCE: The proposed entropy-based measurement, which can be calculated in seconds to minutes in most cases, provides a rapid quantitative evaluation on the limitation of idealized short-read genome sequencing. Moreover, the calculation can be parallelized to scale up to large euakryotic genomes. This approach may be useful to tune the sequencing parameters to achieve better genome assemblies when a closely related genome is already available.

  6. Gas temperature measurements in short duration turbomachinery test facilities

    Science.gov (United States)

    Cattafesta, L. N.; Epstein, A. H.

    1988-07-01

    Thermocouple rakes for use in short-duration turbomachinery test facilities have been developed using very fine thermocouples. Geometry variations were parametrically tested and showed that bare quartz junction supports (76 microns in diameter) yielded superior performance, and were rugged enough to survive considerable impact damage. Using very low cost signal conditioning electronics, temperature accuracies of 0.3 percent were realized yielding turbine efficiency measurements at the 1-percent level. Ongoing work to improve this accuracy is described.

  7. Hypothesis testing in students: Sequences, stages, and instructional strategies

    Science.gov (United States)

    Moshman, David; Thompson, Pat A.

    Six sequences in the development of hypothesis-testing conceptions are proposed, involving (a) interpretation of the hypothesis; (b) the distinction between using theories and testing theories; (c) the consideration of multiple possibilities; (d) the relation of theory and data; (e) the nature of verification and falsification; and (f) the relation of truth and falsity. An alternative account is then provided involving three global stages: concrete operations, formal operations, and a postformal metaconstructivestage. Relative advantages and difficulties of the stage and sequence conceptualizations are discussed. Finally, three families of teaching strategy are distinguished, which emphasize, respectively: (a) social transmission of knowledge; (b) carefully sequenced empirical experience by the student; and (c) self-regulated cognitive activity of the student. It is argued on the basis of Piaget's theory that the last of these plays a crucial role in the construction of such logical reasoning strategies as those involved in testing hypotheses.

  8. Screening of SHOX gene sequence variants in Saudi Arabian children with idiopathic short stature.

    Science.gov (United States)

    Alharthi, Abdulla A; El-Hallous, Ehab I; Talaat, Iman M; Alghamdi, Hamed A; Almalki, Matar I; Gaber, Ahmed

    2017-10-01

    Short stature affects approximately 2%-3% of children, representing one of the most frequent disorders for which clinical attention is sought during childhood. Despite assumed genetic heterogeneity, mutations or deletions in the short stature homeobox-containing gene ( SHOX ) are frequently detected in subjects with short stature. Idiopathic short stature (ISS) refers to patients with short stature for various unknown reasons. The goal of this study was to screen all the exons of SHOX to identify related mutations. We screened all the exons of SHOX for mutations analysis in 105 ISS children patients (57 girls and 48 boys) living in Taif governorate, KSA using a direct DNA sequencing method. Height, arm span, and sitting height were recorded, and subischial leg length was calculated. A total of 30 of 105 ISS patients (28%) contained six polymorphic variants in exons 1, 2, 4, and 6. One mutation was found in the DNA domain binding region of exon 4. Three of these polymorphic variants were novel, while the others were reported previously. There were no significant differences in anthropometric measures in ISS patients with and without identifiable polymorphic variants in SHOX . In Saudi Arabia ISS patients, rather than SHOX , it is possible that new genes are involved in longitudinal growth. Additional molecular analysis is required to diagnose and understand the etiology of this disease.

  9. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

    Science.gov (United States)

    Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

    2018-01-01

    Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also

  10. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2014-01-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  11. Keeping it together: Semantic coherence stabilizes phonological sequences in short-term memory.

    Science.gov (United States)

    Savill, Nicola; Ellis, Rachel; Brooke, Emma; Koa, Tiffany; Ferguson, Suzie; Rojas-Rodriguez, Elena; Arnold, Dominic; Smallwood, Jonathan; Jefferies, Elizabeth

    2018-04-01

    Our ability to hold a sequence of speech sounds in mind, in the correct configuration, supports many aspects of communication, but the contribution of conceptual information to this basic phonological capacity remains controversial. Previous research has shown modest and inconsistent benefits of meaning on phonological stability in short-term memory, but these studies were based on sets of unrelated words. Using a novel design, we examined the immediate recall of sentence-like sequences with coherent meaning, alongside both standard word lists and mixed lists containing words and nonwords. We found, and replicated, substantial effects of coherent meaning on phoneme-level accuracy: The phonemes of both words and nonwords within conceptually coherent sequences were more likely to be produced together and in the correct order. Since nonwords do not exist as items in long-term memory, the semantic enhancement of phoneme-level recall for both item types cannot be explained by a lexically based item reconstruction process employed at the point of retrieval ("redintegration"). Instead, our data show, for naturalistic input, that when meaning emerges from the combination of words, the phonological traces that support language are reinforced by a semantic-binding process that has been largely overlooked by past short-term memory research.

  12. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.

    Science.gov (United States)

    Pericard, Pierre; Dufresne, Yoann; Couderc, Loïc; Blanquart, Samuel; Touzet, Hélène

    2018-02-15

    Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution. We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments. https://github.com/bonsai-team/matam. pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  13. CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs.

    Science.gov (United States)

    Gilbert, N; Labuda, D

    1999-03-16

    A 65-bp "core" sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3' ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome.

  14. X-ray testing for short-time dynamic applications

    International Nuclear Information System (INIS)

    Kurfiss, Malte; Moser, Stefan; Popko, Gregor; Nau, Siegfried

    2017-01-01

    For nondestructive testing purposes new challenges are short-time dynamic processes. The application of x-ray flash tubes and modern high-speed cameras allows the observation of the opening of air-bags or the energy absorption of compressed tubes as occurring during a vehicle crash. Special algorithms designed for computerized tomography analyses allow the 3D reconstruction at individual time points of the dynamic process. Possibilities and limitations of the actual techniques are discussed.

  15. Vietnamese validation of the short version of Internet Addiction Test

    OpenAIRE

    Tran, Bach Xuan; Mai, Hue Thi; Nguyen, Long Hoang; Nguyen, Cuong Tat; Latkin, Carl A.; Zhang, Melvyn W.B.; Ho, Roger C.M.

    2017-01-01

    Background and aims: The main goal of the present study was to examine the psychometric properties of a Vietnamese version of the short-version of Internet Addiction Test (s-IAT) and to assess the relationship between s-IAT scores and demographics, health related qualify of life and perceived stress scores in young Vietnamese. Methods: The Vietnamese version of s-IAT was administered to a sample of 589 participants. Exploratory factor and reliability analyses were performed. Regression analys...

  16. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  17. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Science.gov (United States)

    Nowrousian, Minou; Stajich, Jason E; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D; Pöggeler, Stefanie; Read, Nick D; Seiler, Stephan; Smith, Kristina M; Zickler, Denise; Kück, Ulrich; Freitag, Michael

    2010-04-08

    Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for

  18. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Directory of Open Access Journals (Sweden)

    Minou Nowrousian

    2010-04-01

    Full Text Available Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data

  19. Effects of High Intensity White Noise on Short-Term Memory for Position in a List and Sequence

    Science.gov (United States)

    Daee, Safar; Wilding, J. M.

    1977-01-01

    Seven experiments are described investigating the effecy of high intensity white noise during the visual presentation of words on a number of short-term memory tasks. Examines results relative to position learning and sequence learning. (Editor/RK)

  20. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  1. Efficient and controllable thermal ablation induced by short-pulsed HIFU sequence assisted with perfluorohexane nanodroplets.

    Science.gov (United States)

    Chang, Nan; Lu, Shukuan; Qin, Dui; Xu, Tianqi; Han, Meng; Wang, Supin; Wan, Mingxi

    2018-07-01

    A HIFU sequence with extremely short pulse duration and high pulse repetition frequency can achieve thermal ablation at a low acoustic power using inertial cavitation. Because of its cavitation-dependent property, the therapeutic outcome is unreliable when the treatment zone lacks cavitation nuclei. To overcome this intrinsic limitation, we introduced perfluorocarbon nanodroplets as extra cavitation nuclei into short-pulsed HIFU-mediated thermal ablation. Two types of nanodroplets were used with perfluorohexane (PFH) as the core material coated with bovine serum albumin (BSA) or an anionic fluorosurfactant (FS) to demonstrate the feasibility of this study. The thermal ablation process was recorded by high-speed photography. The inertial cavitation activity during the ablation was revealed by sonoluminescence (SL). The high-speed photography results show that the thermal ablation volume increased by ∼643% and 596% with BSA-PFH and FS-PFH, respectively, than the short-pulsed HIFU alone at an acoustic power of 19.5 W. Using nanodroplets, much larger ablation volumes were created even at a much lower acoustic power. Meanwhile, the treatment time for ablating a desired volume significantly reduced in the presence of nanodroplets. Moreover, by adjusting the treatment time, lesion migration towards the HIFU transducer could also be avoided. The SL results show that the thermal lesion shape was significantly dependent on the inertial cavitation in this short-pulsed HIFU-mediated thermal ablation. The inertial cavitation activity became more predictable by using nanodroplets. Therefore, the introduction of PFH nanodroplets as extra cavitation nuclei made the short-pulsed HIFU thermal ablation more efficient by increasing the ablation volume and speed, and more controllable by reducing the acoustic power and preventing lesion migration. Copyright © 2018. Published by Elsevier B.V.

  2. Prospective testing of Coulomb short-term earthquake forecasts

    Science.gov (United States)

    Jackson, D. D.; Kagan, Y. Y.; Schorlemmer, D.; Zechar, J. D.; Wang, Q.; Wong, K.

    2009-12-01

    Earthquake induced Coulomb stresses, whether static or dynamic, suddenly change the probability of future earthquakes. Models to estimate stress and the resulting seismicity changes could help to illuminate earthquake physics and guide appropriate precautionary response. But do these models have improved forecasting power compared to empirical statistical models? The best answer lies in prospective testing in which a fully specified model, with no subsequent parameter adjustments, is evaluated against future earthquakes. The Center of Study of Earthquake Predictability (CSEP) facilitates such prospective testing of earthquake forecasts, including several short term forecasts. Formulating Coulomb stress models for formal testing involves several practical problems, mostly shared with other short-term models. First, earthquake probabilities must be calculated after each “perpetrator” earthquake but before the triggered earthquakes, or “victims”. The time interval between a perpetrator and its victims may be very short, as characterized by the Omori law for aftershocks. CSEP evaluates short term models daily, and allows daily updates of the models. However, lots can happen in a day. An alternative is to test and update models on the occurrence of each earthquake over a certain magnitude. To make such updates rapidly enough and to qualify as prospective, earthquake focal mechanisms, slip distributions, stress patterns, and earthquake probabilities would have to be made by computer without human intervention. This scheme would be more appropriate for evaluating scientific ideas, but it may be less useful for practical applications than daily updates. Second, triggered earthquakes are imperfectly recorded following larger events because their seismic waves are buried in the coda of the earlier event. To solve this problem, testing methods need to allow for “censoring” of early aftershock data, and a quantitative model for detection threshold as a function of

  3. Effects of Repeated Testing on Short- and Long-Term Memory Performance across Different Test Formats

    Science.gov (United States)

    Stenlund, Tova; Sundström, Anna; Jonsson, Bert

    2016-01-01

    This study examined whether practice testing with short-answer (SA) items benefits learning over time compared to practice testing with multiple-choice (MC) items, and rereading the material. More specifically, the aim was to test the hypotheses of "retrieval effort" and "transfer appropriate processing" by comparing retention…

  4. Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

    Science.gov (United States)

    Baichoo, Shakuntala; Ouzounis, Christos A

    A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Short Circuit Tests First Step of LHC Hardware Commissioning Completion

    CERN Document Server

    Barbero-Soto, E; Bordry, Frederick; Casas Lino, M P; Coelingh, G J; Cumer, G; Dahlerup-Petersen, K; Guillaume, J C; Inigo-Golfin, J; Montabonnet, V; Nisbet, D; Pojer, M; Principe, R; Rodríguez-Mateos, F; Saban, R; Schmidt, R; Thiesen, H; Vergara-Fernández, A; Zerlauth, M; Castaneda Serra, A; Romera Ramirez, I

    2008-01-01

    For the two counter rotating beams in the Large Hadron Collider (LHC) about 8000 magnets (main dipole and quadrupole magnets, corrector magnets, separation dipoles, matching section quadrupoles etc.) are powered in about 1500 superconducting electrical circuits. The magnets are powered by power converters that have been designed for the LHC with a current between 60 and 13000A. Between October 2005 and September 2007 the so-called Short Circuit Tests were carried-out in 15 underground zones where the power converters of the superconducting circuits are placed. The tests aimed to qualify the normal conducting equipments of the circuits such as power converters and normal conducting high current cables. The correct operation of interlock and energy extraction systems was validated. The infrastructure systems including AC distribution, water and air cooling and the control systems was also commissioned. In this paper the results of the two year test campaign are summarized with particular attention to problems e...

  6. Short term mutagenicity tests and their application to irradiated foods

    International Nuclear Information System (INIS)

    Phillips, B.J.; Elias, P.S.

    1980-01-01

    Although traditional long-term animal tests are likely to continue to be required, these are not only extremely costly but are coming more and more to be recognised as an imprecise and unsatisfactory method of testing the safety of irradiated foods for human consumption. It is therefore clearly advisable to include a selection of quicker and more direct testing methods in any toxicological assessment procedures. The International Project has therefore undertaken a study of the feasibility of using the newer systems for investigation of irradiated foodstuffs. Although some work in this field has already been carried out, some shortcomings in the published work can be identified which justify a more detailed and intensive research programme. As expected, little difficulty has been encountered in testing food by methods involving mammals, but considerable effort has been required to adapt in vitro systems. The use of enzymatic digestion in vitro to provide food samples for testing in mammalian cell cultures has never been attempted before and the procedures developed by the Project represent a positive contribution to methodology in this field. A series of foodstuffs is being tested by a wide spectrum of short-term tests and the first results are now being obtained. (orig./MG) [de

  7. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

    DEFF Research Database (Denmark)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo

    2012-01-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp...... these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species....

  8. Experimental tests of induced spatial incoherence using short laser wavelength

    International Nuclear Information System (INIS)

    Obenschain, S.P.; Grun, J.; Herbst, M.J.

    1986-01-01

    The authors have developed a laser beam smoothing technique called induced spatial incoherence (ISI), which can produce the highly uniform focal profiles required for direct-drive laser fusion. Uniform well-controlled focal profiles are required to obtain the highly symmetric pellet implosions needed for high-energy gain. In recent experiments, the authors' tested the effects of ISI on high-power laser-target interaction. With short laser wavelength, the coupling physics dramatically improved over that obtained with an ordinary laser beam

  9. Study of the fast inversion recovery pulse sequence. With reference to fast fluid attenuated inversion recovery and fast short TI inversion recovery pulse sequence

    International Nuclear Information System (INIS)

    Tsuchihashi, Toshio; Maki, Toshio; Suzuki, Takeshi

    1997-01-01

    The fast inversion recovery (fast IR) pulse sequence was evaluated. We compared the fast fluid attenuated inversion recovery (fast FLAIR) pulse sequence in which inversion time (TI) was established as equal to the water null point for the purpose of the water-suppressed T 2 -weighted image, with the fast short TI inversion recovery (fast STIR) pulse sequence in which TI was established as equal to the fat null point for purpose of fat suppression. In the fast FLAIR pulse sequence, the water null point was increased by making TR longer. In the FLAIR pulse sequence, the longitudinal magnetization contrast is determined by TI. If TI is increased, T 2 -weighted contrast improves in the same way as increasing TR for the SE pulse sequence. Therefore, images should be taken with long TR and long TI, which are longer than TR and longer than the water null point. On the other hand, the fat null point is not affected by TR in the fast STIR pulse sequence. However, effective TE was affected by variation of the null point. This increased in proportion to the increase in effective TE. Our evaluation indicated that the fast STIR pulse sequence can control the extensive signals from fat in a short time. (author)

  10. Vietnamese validation of the short version of Internet Addiction Test

    Directory of Open Access Journals (Sweden)

    Bach Xuan Tran

    2017-12-01

    Full Text Available Background and aims: The main goal of the present study was to examine the psychometric properties of a Vietnamese version of the short-version of Internet Addiction Test (s-IAT and to assess the relationship between s-IAT scores and demographics, health related qualify of life and perceived stress scores in young Vietnamese. Methods: The Vietnamese version of s-IAT was administered to a sample of 589 participants. Exploratory factor and reliability analyses were performed. Regression analysis was used to identify the associated factors. Results: The two-factor model of Vietnamese version of s-IAT demonstrated good psychometric properties. The internal consistency of Factor 1 (loss of control/time management was high (Cronbach's alpha=0.82 and Factor 2 (craving/social problems was satisfactory (Cronbach's alpha=0.75. Findings indicated that 20.9% youths were addicted to the Internet. Regression analysis revealed significant associations between Internet addiction and having problems in self-care, lower quality of life and high perceived stress scores. Discussion and conclusions: The Vietnamese version of s-IAT is a valid and reliable instrument to assess IA in Vietnamese population. Due to the high prevalence of IA among Vietnamese youths, IA should be paid attention in future intervention programs. s-IAT can be a useful screening tool for IA to promptly inform and treat the IA among Vietnamese youths. Keywords: Factor analysis, Short-version, Internet Addiction Test, Psychometric properties, Vietnamese

  11. Exact association test for small size sequencing data.

    Science.gov (United States)

    Lee, Joowon; Lee, Seungyeoun; Jang, Jin-Young; Park, Taesung

    2018-04-20

    Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e.g., burden tests and variance-component tests) rely on large sample sizes. Notwithstanding, due to its-still high cost, NGS data is generally restricted to small sample sizes, that cannot be analyzed by most existing methods. In this work, we propose a new exact association test for sequencing data that does not require a large sample approximation, which is applicable to both common and rare variants. Our method, based on the Generalized Cochran-Mantel-Haenszel (GCMH) statistic, was applied to NGS datasets from intraductal papillary mucinous neoplasm (IPMN) patients. IPMN is a unique pancreatic cancer subtype that can turn into an invasive and hard-to-treat metastatic disease. Application of our method to IPMN data successfully identified susceptible genes associated with progression of IPMN to pancreatic cancer. Our method is expected to identify disease-associated genetic variants more successfully, and corresponding signal pathways, improving our understanding of specific disease's etiology and prognosis.

  12. Short-term static corrosion tests in lead-bismuth

    Science.gov (United States)

    Soler Crespo, L.; Martín Muñoz, F. J.; Gómez Briceño, D.

    2001-07-01

    Martensitic steels have been proposed to be used as structural materials and as spallation target window in hybrid systems devoted to the transmutation of radioactive waste of long life and high activity. However, their compatibility with lead-bismuth in the operating conditions of these systems depends on the existence of a protective layer such as an oxide film. The feasibility of forming and maintaining an oxide layer or maintaining a pre-oxidised one has been studied. Martensitic steel F82Hmod. (8% Cr) has been tested in lead-bismuth under static and isothermal conditions at 400°C and 600°C. In order to study the first stages of the interaction between the steel and the eutectic, short-term tests (100 and 665 h) have been carried out. Pre-oxidised and as-received samples have been tested in atmospheres with different oxidant potential. For low oxygen concentration in lead-bismuth due to unexpected oxygen consumption in the experimental device, dissolution of as-received F82Hmod. occurs and pre-oxidation does not prevent the material dissolution. For high oxygen concentration, the pre-oxidation layer seems to improve the feasibility of protecting stainless steels controlling the oxygen potential of lead-bismuth with a gas phase.

  13. Short-term static corrosion tests in lead-bismuth

    International Nuclear Information System (INIS)

    Soler Crespo, L.; Martin Munoz, F.J.; Gomez Briceno, D.

    2001-01-01

    Martensitic steels have been proposed to be used as structural materials and as spallation target window in hybrid systems devoted to the transmutation of radioactive waste of long life and high activity. However, their compatibility with lead-bismuth in the operating conditions of these systems depends on the existence of a protective layer such as an oxide film. The feasibility of forming and maintaining an oxide layer or maintaining a pre-oxidised one has been studied. Martensitic steel F82Hmod. (8% Cr) has been tested in lead-bismuth under static and isothermal conditions at 400 o C and 600 o C. In order to study the first stages of the interaction between the steel and the eutectic, short-term tests (100 and 665 h) have been carried out. Pre-oxidised and as-received samples have been tested in atmospheres with different oxidant potential. For low oxygen concentration in lead-bismuth due to unexpected oxygen consumption in the experimental device, dissolution of as-received F82Hmod. occurs and pre-oxidation does not prevent the material dissolution. For high oxygen concentration, the pre-oxidation layer seems to improve the feasibility of protecting stainless steels controlling the oxygen potential of lead-bismuth with a gas phase

  14. Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts.

    Science.gov (United States)

    Cerveau, Nicolas; Leclercq, Sébastien; Leroy, Elodie; Bouchon, Didier; Cordaux, Richard

    2011-01-01

    Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52-171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes.

  15. Validation of a Short Form of an Indecision Test: The Vocational Assessment Test

    Science.gov (United States)

    Picard, France; Frenette, Éric; Guay, Frédéric; Labrosse, Julie

    2015-01-01

    The purpose of this research was to validate the scores of a short form of a new instrument, "l'Épreuve de décision vocationnelle, forme scolaire" (EDV-9S; vocational assessment test), which measures six indecision-related problems (lack of self-knowledge, lack of readiness, lack of method in decision making, lack of information,…

  16. Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data.

    Science.gov (United States)

    Szymanski, Maciej; Karlowski, Wojciech M

    2016-01-01

    In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.

  17. Vietnamese validation of the short version of Internet Addiction Test.

    Science.gov (United States)

    Tran, Bach Xuan; Mai, Hue Thi; Nguyen, Long Hoang; Nguyen, Cuong Tat; Latkin, Carl A; Zhang, Melvyn W B; Ho, Roger C M

    2017-12-01

    The main goal of the present study was to examine the psychometric properties of a Vietnamese version of the short-version of Internet Addiction Test (s-IAT) and to assess the relationship between s-IAT scores and demographics, health related qualify of life and perceived stress scores in young Vietnamese. The Vietnamese version of s-IAT was administered to a sample of 589 participants. Exploratory factor and reliability analyses were performed. Regression analysis was used to identify the associated factors. The two-factor model of Vietnamese version of s-IAT demonstrated good psychometric properties. The internal consistency of Factor 1 (loss of control/time management) was high (Cronbach's alpha = 0.82) and Factor 2 (craving/social problems) was satisfactory (Cronbach's alpha = 0.75). Findings indicated that 20.9% youths were addicted to the Internet. Regression analysis revealed significant associations between Internet addiction and having problems in self-care, lower quality of life and high perceived stress scores. The Vietnamese version of s-IAT is a valid and reliable instrument to assess IA in Vietnamese population. Due to the high prevalence of IA among Vietnamese youths, IA should be paid attention in future intervention programs. s-IAT can be a useful screening tool for IA to promptly inform and treat the IA among Vietnamese youths.

  18. Resonant magnetoelectric response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    Directory of Open Access Journals (Sweden)

    Matthias C. Krantz

    2015-11-01

    Full Text Available The magnetoelectric effect in layered composite cantilevers consisting of strain coupled layers of magnetostrictive (MS, piezoelectric (PE, and substrate materials is investigated for magnetic field excitation at bending resonance. Analytic theories are derived for the transverse magnetoelectric (ME response in short and open circuit operation for three different layer sequences and results presented and discussed for the FeCoBSi-AlN-Si and the FeCoBSi-PZT-Si composite systems. Response optimized PE-MS layer thickness ratios are found to greatly change with operation mode shifting from near equal MS and PE layer thicknesses in the open circuit mode to near vanishing PE layer thicknesses in short circuit operation for all layer sequences. In addition the substrate layer thickness is found to differently affect the open and short circuit ME response producing shifts and reversal between ME response maxima depending on layer sequence. The observed rich ME response behavior for different layer thicknesses, sequences, operating modes, and PE materials can be explained by common neutral plane effects and different elastic compliance effects in short and open circuit operation.

  19. [Possibilities in the differential diagnosis of brain neoplasms using the long and short time sequences of proton magnetic resonance spectroscopy

    NARCIS (Netherlands)

    Gajewicz, W.; Goraj, B.M.

    2004-01-01

    Currently to perform proton magnetic resonance spectroscopy (1H MRS) with single voxel spectroscopy (SVS) technique long and/or short echo time sequences are used in order to provide complementary information. PURPOSE: The aim of the study was to compare the usefulness of STEAM (time echo, TE, 20

  20. Short (

    NARCIS (Netherlands)

    Telleman, Gerdien; den Hartog, Laurens

    2013-01-01

    Aim: This systematic review assessed the implant survival rate of short (<10 mm) dental implants installed in partially edentulous patients. A case report of a short implant in the posterior region have been added. Materials and methods: A search was conducted in the electronic databases of MEDLINE

  1. Approaching Repetitive Short Circuit Tests on MW-Scale Power Modules by means of an Automatic Testing Setup

    DEFF Research Database (Denmark)

    Reigosa, Paula Diaz; Wang, Huai; Iannuzzo, Francesco

    2016-01-01

    An automatic testing system to perform repetitive short-circuit tests on megawatt-scale IGBT power modules is pre-sented and described in this paper, pointing out the advantages and features of such testing approach. The developed system is based on a non-destructive short-circuit tester, which has...

  2. Isolation and amino acid sequence of a short-chain neurotoxin from an Australian elapid snake, Pseudechis australis.

    OpenAIRE

    Takasaki, C; Tamiya, N

    1985-01-01

    A short-chain neurotoxin Pseudechis australis a (toxin Pa a) was isolated from the venom of an Australian elapid snake Pseudechis australis (king brown snake) by sequential chromatography on CM-cellulose, Sephadex G-50 and CM-cellulose columns. Toxin Pa a has an LD50 (intravenous) value of 76 micrograms/kg body wt. in mice and consists of 62 amino acid residues. The amino acid sequence of Pa a shows considerable homology with those of short-chain neurotoxins of elapid snakes, especially of tr...

  3. Experience of targeted Usher exome sequencing as a clinical test

    Science.gov (United States)

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  4. Convolutional neural network regression for short-axis left ventricle segmentation in cardiac cine MR sequences.

    Science.gov (United States)

    Tan, Li Kuo; Liew, Yih Miin; Lim, Einly; McLaughlin, Robert A

    2017-07-01

    Automated left ventricular (LV) segmentation is crucial for efficient quantification of cardiac function and morphology to aid subsequent management of cardiac pathologies. In this paper, we parameterize the complete (all short axis slices and phases) LV segmentation task in terms of the radial distances between the LV centerpoint and the endo- and epicardial contours in polar space. We then utilize convolutional neural network regression to infer these parameters. Utilizing parameter regression, as opposed to conventional pixel classification, allows the network to inherently reflect domain-specific physical constraints. We have benchmarked our approach primarily against the publicly-available left ventricle segmentation challenge (LVSC) dataset, which consists of 100 training and 100 validation cardiac MRI cases representing a heterogeneous mix of cardiac pathologies and imaging parameters across multiple centers. Our approach attained a .77 Jaccard index, which is the highest published overall result in comparison to other automated algorithms. To test general applicability, we also evaluated against the Kaggle Second Annual Data Science Bowl, where the evaluation metric was the indirect clinical measures of LV volume rather than direct myocardial contours. Our approach attained a Continuous Ranked Probability Score (CRPS) of .0124, which would have ranked tenth in the original challenge. With this we demonstrate the effectiveness of convolutional neural network regression paired with domain-specific features in clinical segmentation. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Short Interspersed Nuclear Element (SINE Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293.

    Directory of Open Access Journals (Sweden)

    Lakkhana Kanhayuwa

    Full Text Available Novel families of short interspersed nuclear element (SINE sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.

  6. Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293.

    Science.gov (United States)

    Kanhayuwa, Lakkhana; Coutts, Robert H A

    2016-01-01

    Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.

  7. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    DEFF Research Database (Denmark)

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas

    2014-01-01

    nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior...

  8. Genomic Sequence of a Ranavirus Isolated from Short-Finned Eel (Anguilla australis)

    DEFF Research Database (Denmark)

    Subramaniam, Kuttichantran; Toffan, Anna; Cappellozza, Elisabetta

    2016-01-01

    The short-finned eel ranavirus (SERV) was isolated from short-finned eel imported to Italy from New Zealand. Phylogenomic analyses revealed that SERV is a unique member of the genus Ranavirus, family Iridoviridae, branching at the base of the tree near other fish ranaviruses....

  9. BarraCUDA - a fast short read sequence aligner using graphics processing units

    Directory of Open Access Journals (Sweden)

    Klus Petr

    2012-01-01

    Full Text Available Abstract Background With the maturation of next-generation DNA sequencing (NGS technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU, extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net

  10. BarraCUDA - a fast short read sequence aligner using graphics processing units

    LENUS (Irish Health Repository)

    Klus, Petr

    2012-01-13

    Abstract Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http:\\/\\/seqbarracuda.sf.net

  11. Musicians' and nonmusicians' short-term memory for verbal and musical sequences: comparing phonological similarity and pitch proximity.

    Science.gov (United States)

    Williamson, Victoria J; Baddeley, Alan D; Hitch, Graham J

    2010-03-01

    Language-music comparative studies have highlighted the potential for shared resources or neural overlap in auditory short-term memory. However, there is a lack of behavioral methodologies for comparing verbal and musical serial recall. We developed a visual grid response that allowed both musicians and nonmusicians to perform serial recall of letter and tone sequences. The new method was used to compare the phonological similarity effect with the impact of an operationalized musical equivalent-pitch proximity. Over the course of three experiments, we found that short-term memory for tones had several similarities to verbal memory, including limited capacity and a significant effect of pitch proximity in nonmusicians. Despite being vulnerable to phonological similarity when recalling letters, however, musicians showed no effect of pitch proximity, a result that we suggest might reflect strategy differences. Overall, the findings support a limited degree of correspondence in the way that verbal and musical sounds are processed in auditory short-term memory.

  12. Short-term consistency testing vs. long-term behavior

    International Nuclear Information System (INIS)

    Ebert, W.L.; Bakel, A.J.; Wolf, S.F.; Strachan, D.M.

    1997-01-01

    The authors conducted Product Consistency Tests (PCTs) with a surrogate low-activity waste (LAW) glass to (1) evaluate the possible use of various test conditions in a specification test for LAW waste forms, (2) measure the reproducibility of the test at low temperatures, and (3) determine if the rates calculated from 7-day PCTs bound the rates measured in PCT conducted for longer durations, which represent more advanced corrosion. The effects of temperature and pH on the dissolution rate in PCTs are much less than the effects observed in dilute solutions due to the buildup of dissolved glass components in the PCTs. The precision of replicate 7-day tests at 20 and 40 degrees C was limited by the analytical uncertainty. The dissolution rates at all temperatures decreased with the test duration initially. However, the dissolution rates in tests at 70 and 90 degrees C increased when certain alteration phases formed after about 100 and 500 days, respectively; the rates in some tests exceeded that measured in a 7-day PCT. While the 7-day PCT does not provide a bounding rate for this glass at 70 or 90 degrees C, tests for longer durations are needed to determine if a 7-day test provides a bounding rate at lower temperatures

  13. Quality Control Test for Sequence-Phenotype Assignments

    Science.gov (United States)

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  14. RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing.

    Directory of Open Access Journals (Sweden)

    Fenggang Li

    Full Text Available The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp. Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR. The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.

  15. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.

    Directory of Open Access Journals (Sweden)

    Christopher A Miller

    2011-01-01

    Full Text Available Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/.

  16. Tests for nonlinearity in short stationary time series

    International Nuclear Information System (INIS)

    Chang, T.; Sauer, T.; Schiff, S.J.

    1995-01-01

    To compare direct tests for detecting determinism in chaotic time series, data from Henon, Lorenz, and Mackey--Glass equations were contaminated with various levels of additive colored noise. These data were analyzed with a variety of recently developed tests for determinism, and the results compared

  17. Short Report Challenges with targeted viral load testing for medical ...

    African Journals Online (AJOL)

    Challenges with targeted viral load testing 179. Malawi Medical ... targeted viral load (VL) testing for patients who have been on ART for at least .... Tuberculosis. 32. Community-acquired pneumonia. 17. Non-typhoidal Salmonella sepsis. 5. Bacterial meningitis. 5. Disseminated Kaposi sarcoma. 4. Cryptococcal meningitis. 4.

  18. Fourteen years of test experience with short-circuit withstand capability of large power transformers

    NARCIS (Netherlands)

    Smeets, R.P.P.; Paske, te L.H.

    2010-01-01

    Experience is reported of short-circuit testing of large power transformers during the past 14 years by KEMA in the Netherlands. In total, 119 transformers > 25 MVA participated in the survey. KEMA shows that at initial access to standard IEC short-circuit tests, 28% failed initially in a wide range

  19. Sixteen years of test experiences with short-circuit withstand capability of large power transformers

    NARCIS (Netherlands)

    Smeets, R.P.P.; Paske, te L.H.

    2012-01-01

    Experience is reported of short-circuit testing of large power transformers during the past 16 years by KEMA in the Netherlands. In total, 174 transformers > 25 MVA participated in the survey. KEMA shows that at initial access to standard IEC short-circuit tests, 24% failed initially in a wide range

  20. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

    Directory of Open Access Journals (Sweden)

    Trimble William L

    2012-07-01

    Full Text Available Abstract Background Gene prediction algorithms (or gene callers are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp fragments containing sequence error from previously published artificial data and “real” metagenomic datasets. Results While gene prediction tools have similar accuracies predicting genes on error-free fragments, in the presence of sequencing errors considerable differences between tools become evident. For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal. This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50% specificity and overprediction of genes in noncoding regions. Conclusions Ab initio gene callers offer a significant reduction in the computational burden of annotating individual nucleic acid reads and are used in many metagenomic annotation systems. For predicting reading frames on raw reads, we find the hidden Markov model approach in FragGeneScan is more sensitive than other gene prediction tools, while Prodigal, MGA, and MGM are better suited for higher-quality sequences such as assembled contigs.

  1. Relationship Between Short Sleep Duration and Preseason Concussion Testing.

    Science.gov (United States)

    Silverberg, Noah D; Berkner, Paul D; Atkins, Joseph E; Zafonte, Ross; Iverson, Grant L

    2016-05-01

    Baseline, preseason assessment of cognition, symptoms, and balance has been recommended as part of a comprehensive sport concussion management program. We examined the relationship between sleep and baseline test results. We hypothesized that adolescents who slept fewer hours the night before would report more symptoms and perform more poorly on cognitive testing than students who had a full night sleep. Cross-sectional observation study. Preseason concussion testing for high school athletes. A large sample (n = 2928) of student athletes from Maine, USA, between the ages of 13 and 18 years completed preseason testing. Participants with developmental problems, a history of treatment for neurological or psychiatric problems, recent concussion, or 3 or more prior concussions were excluded. Athletes were divided into 4 groups based on their sleep duration the night before testing. Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT; ImPACT Applications, Inc, Pittsburgh, PA) cognitive composite scores and the embedded Post-Concussion Symptom Scale. Sleep was not related to any ImPACT cognitive composite score, after covarying for age and controlling for multiple comparisons. In contrast, there were sleep duration, sex, and sleep duration by sex effects on the Post-Concussion Symptom Scale. The effect of sleep duration on symptom reporting was more pronounced in girls. Supplementary analyses suggested that sleep insufficiency was associated with a diverse array of postconcussion-like symptoms. Poor sleep the night before baseline or postinjury testing may be an important confound when assessing postconcussion symptoms. Girls may be more vulnerable to experiencing and reporting symptoms following insufficient sleep. Clinicians should routinely ask how the athlete slept the night before preseason baseline testing and consider deferring the symptom assessment or later retesting athletes who slept poorly.

  2. Temporal Clustering and Sequencing in Short-Term Memory and Episodic Memory

    Science.gov (United States)

    Farrell, Simon

    2012-01-01

    A model of short-term memory and episodic memory is presented, with the core assumptions that (a) people parse their continuous experience into episodic clusters and (b) items are clustered together in memory as episodes by binding information within an episode to a common temporal context. Along with the additional assumption that information…

  3. Quality Testing of Short Rotation Coppice Willow Cuttings

    Directory of Open Access Journals (Sweden)

    Katrin Heinsoo

    2018-06-01

    Full Text Available The production and feasibility of Short Rotation Coppice depend on cutting early performance. The shoot and root biomass production of Salix cuttings in hydroponic conditions was studied. The amount of sprouted biomass after four weeks of growth depended on cutting the diameter, but the original position of the cutting along the rod or number of visible buds was not in correlation with biomass produced. Application of mineral fertilizer or soil originating from the willow plantation did not increase the total production. On the contrary, the addition of soil tended to decrease biomass production and we assumed this was a result of a shortage of light. Under the influence of fertilization, plants allocated greater biomass to roots. Comparison of different clones revealed that those with S. dasyclados genes tended to allocate less biomass to roots and the poorest-performing clone in our experiment, also had the lowest wood production in the plantation. The number of visible buds on the cutting was also clone-specific.

  4. Short-Cut Estimators of Criterion-Referenced Test Consistency.

    Science.gov (United States)

    Brown, James Dean

    1990-01-01

    Presents simplified methods for deriving estimates of the consistency of criterion-referenced, English-as-a-Second-Language tests, including (1) the threshold loss agreement approach using agreement or kappa coefficients, (2) the squared-error loss agreement approach using the phi(lambda) dependability approach, and (3) the domain score…

  5. Far-UV-induced dimeric photoproducts in short oligonucleotides: sequence effects

    International Nuclear Information System (INIS)

    Douki, T.; Zalizniak, T.; Cadet, J.

    1997-01-01

    Cyclobutane pyrimidine dimers and pyrimidine (6-4)pyrimidone adducts represent the two major classes of far-UV-induced DNA photoproducts. Because of the lack of appropriate detection methods for each individual photoproduct, little is known about the effect of the sequence on their formaiton. In the present work, the photoproduct distribution obtained upon exposure of a series of dinucleoside monophosphate to 254 nm light was determined. (author)

  6. [Topographic mapping of retinal function with a scanning laser ophthalmoscope and multifocal electroretinography using short M-sequences].

    Science.gov (United States)

    Rudolph, G; Bechmann, M; Berninger, T; Kutschbach, E; Held, U; Tornow, R P; Kalpadakis, P; Zol'nikova, I V; Shamshinova, A M

    2001-01-01

    A new method of multifocal electroretinography making use of scanning laser ophthalmoscope with a wavelength of 630 nm (SLO-m-ERG), evoking short spatial visual stimuli on the retina, is proposed. Algorithm of presenting the visual stimuli and analysis of distribution of local electroretinograms on the surface of the retina is based on short m-sequences. Mathematical cross correlation analysis shows a three-dimensional distribution of bioelectrical activity of the retina in the central visual field. In normal subjects the cone bioelectrical activity is the maximum in the macular area (corresponding to the density of cone distribution) and absent in the blind spot. The method detects the slightest pathological changes in the retina under control of the site of stimulation and ophthalmoscopic picture of the fundus oculi. The site of the pathological process correlates with the topography of changes in bioelectrical activity of the examined retinal area in diseases of the macular area and pigmented retinitis detectable by ophthalmoscopy.

  7. Analysing breast tissue composition with MRI using currently available short, simple sequences

    International Nuclear Information System (INIS)

    Chau, A.C.M.; Hua, J.; Taylor, D.B.

    2016-01-01

    Aim: To determine the most robust commonly available magnetic resonance imaging (MRI) sequence to quantify breast tissue composition at 1.5 T. Materials and methods: Two-dimensional (2D) T1-weighted, Dixon fat, Dixon water and SPAIR images were obtained from five participants and a breast phantom using a 1.5 T Siemens Aera MRI system. Manual segmentation of the breasts was performed, and an in-house computer program was used to generate signal intensity histograms. Relative trough depth and relative peak separation were used to determine the robustness of the images for quantifying the two breast tissues. Total breast volumes and percentage breast densities calculated using the four sequences were compared. Results: Dixon fat histograms had consistently low relative trough depth and relative peak separation compared to those obtained using other sequences. There was no significant difference in total breast volumes and percentage breast densities of the participants or breast phantom using Dixon fat and 2D T1-weighted histograms. Dixon water and SPAIR histograms were not suitable for quantifying breast tissue composition. Conclusion: Dixon fat images are the most robust for the quantification of breast tissue composition using a signal intensity histogram. - Highlights: • Signal intensity histogram analysis can determine robustness of images for quantification of breast tissue composition. • Dixon fat images are the most robust. • The characteristics of the signal intensity histograms from Dixon water and SPAIR images make quantification unsuitable.

  8. A facility to test short superconducting accelerator magnets at Fermilab

    International Nuclear Information System (INIS)

    Lamm, M.J.; Hess, C.; Lewis, D.; Jaffery, T.; Kinney, W.; Ozelis, J.P.; Strait, J.; Butteris, J.; McInturff, A.D.; Coulter, K.J.

    1992-10-01

    During the past four years the Superconducting Magnet R ampersand D facility at Fermilab (Lab 2) has successfully tested superconducting dipole, quadrupole, and correction coil magnets less than 2 meters in length for the SSC project and the Tevatron D0/B0 Low-β Insertion. During this time several improvements have been made to the facility that have greatly enhanced its magnet testing capabilities. Among the upgrades have been a new rotating coil and data acquisition system for measuring magnetic fields, a controlled flow liquid helium transfer line using an electronically actuated cryo valve, and stand-alone systems for measuring AC loss and training low current Tevatron correction coil packages. A description of the Lab 2 facilities is presented

  9. [Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

    Science.gov (United States)

    Kramerov, D A; Vasetskiĭ, N S

    2009-01-01

    The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

  10. Whole Genome Sequencing Identifies a Missense Mutation in HES7 Associated with Short Tails in Asian Domestic Cats.

    Science.gov (United States)

    Xu, Xiao; Sun, Xin; Hu, Xue-Song; Zhuang, Yan; Liu, Yue-Chen; Meng, Hao; Miao, Lin; Yu, He; Luo, Shu-Jin

    2016-08-25

    Domestic cats exhibit abundant variations in tail morphology and serve as an excellent model to study the development and evolution of vertebrate tails. Cats with shortened and kinked tails were first recorded in the Malayan archipelago by Charles Darwin in 1868 and remain quite common today in Southeast and East Asia. To elucidate the genetic basis of short tails in Asian cats, we built a pedigree of 13 cats segregating at the trait with a founder from southern China and performed linkage mapping based on whole genome sequencing data from the pedigree. The short-tailed trait was mapped to a 5.6 Mb region of Chr E1, within which the substitution c. 5T > C in the somite segmentation-related gene HES7 was identified as the causal mutation resulting in a missense change (p.V2A). Validation in 245 unrelated cats confirmed the correlation between HES7-c. 5T > C and Chinese short-tailed feral cats as well as the Japanese Bobtail breed, indicating a common genetic basis of the two. In addition, some of our sampled kinked-tailed cats could not be explained by either HES7 or the Manx-related T-box, suggesting at least three independent events in the evolution of domestic cats giving rise to short-tailed traits.

  11. 40 CFR 86.230-11 - Test sequence: general requirements.

    Science.gov (United States)

    2010-07-01

    ... compartment cooling. (1) Fixed speed air cooling of the engine compartment with the compartment cover open... fuel economy testing, alternative engine compartment cooling fans or systems, including those which... test. Additionally, the Administrator may conduct certification, fuel economy and in-use testing using...

  12. 40 CFR 92.124 - Test sequence; general requirements.

    Science.gov (United States)

    2010-07-01

    ... PROGRAMS (CONTINUED) CONTROL OF AIR POLLUTION FROM LOCOMOTIVES AND LOCOMOTIVE ENGINES Test Procedures § 92...) For the testing of locomotives and engines, the atmospheric pressure shall be between 31.0 inches Hg... test conditions. (c) No control of humidity is required for ambient air, engine intake air or dilution...

  13. A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization.

    Science.gov (United States)

    Fossé, P; Motté, N; Roumier, A; Gabus, C; Muriaux, D; Darlix, J L; Paoletti, J

    1996-12-24

    Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5'-ends. Recently, two models have been proposed for RNA dimer formation on the basis of results obtained in vitro with human immunodeficiency virus type 1 RNA and Moloney murine leukemia virus RNA. It was first proposed that viral RNA dimerizes by forming an interstrand quadruple helix with purine tetrads. The second model postulates that RNA dimerization is initiated by a loop-loop interaction between the two RNA molecules. In order to better characterize the dimerization process of retroviral genomic RNA, we analyzed the in vitro dimerization of avian sarcoma-leukosis virus (ASLV) RNA using different transcripts. We determined the requirements for heterodimer formation, the thermal dissociation of RNA dimers, and the influence of antisense DNA oligonucleotides on dimer formation. Our results strongly suggest that purine tetrads are not involved in dimer formation. Data show that an autocomplementary sequence located upstream from the splice donor site and within a major packaging signal plays a crucial role in ASLV RNA dimer formation in vitro. This sequence is able to form a stem-loop structure, and phylogenetic analysis reveals that it is conserved in 28 different avian sarcoma and leukosis viruses. These results suggest that dimerization of ASLV RNA is initiated by a loop-loop interaction between two RNA molecules and provide an additional argument for the ubiquity of the dimerization process via loop-loop interaction.

  14. 40 CFR 86.230-94 - Test sequence: general requirements.

    Science.gov (United States)

    2010-07-01

    ... compartment cooling. (1) Fixed speed air cooling of the engine compartment with the compartment cover open... fuel economy testing, alternative engine compartment cooling fans or systems, including those which... Administrator may conduct certification, fuel economy and in-use testing using the additional cooling set-up...

  15. Application of Next Generation Sequencing on Genetic Testing

    DEFF Research Database (Denmark)

    Li, Jian

    The discovery of genetic factors behind increasing number of human diseases and the growth of education of genetic knowledge to the public make demands for genetic testing increase rapidly. However, traditional genetic testing methods cannot meet all kinds of the requirements. Next generation seq...

  16. A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

    Science.gov (United States)

    Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

    2017-12-01

    - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

  17. Short-duration Electron Precipitation Studied by Test Particle Simulation

    Directory of Open Access Journals (Sweden)

    Jaejin Lee

    2015-12-01

    Full Text Available Energy spectra of electron microbursts from 170 keV to 340 keV have been measured by the solid-state detectors aboard the low-altitude (680 km polar-orbiting Korean STSAT-1 (Science and Technology SATellite. These measurements have revealed two important characteristics unique to the microbursts: (1 They are produced by a fast-loss cone-filling process in which the interaction time for pitch-angle scattering is less than 50 ms and (2 The e-folding energy of the perpendicular component is larger than that of the parallel component, and the loss cone is not completely filled by electrons. To understand how wave-particle interactions could generate microbursts, we performed a test particle simulation and investigated how the waves scattered electron pitch angles within the timescale required for microburst precipitation. The application of rising-frequency whistler-mode waves to electrons of different energies moving in a dipole magnetic field showed that chorus magnetic wave fields, rather than electric fields, were the main cause of microburst events, which implied that microbursts could be produced by a quasi-adiabatic process. In addition, the simulation results showed that high-energy electrons could resonate with chorus waves at high magnetic latitudes where the loss cone was larger, which might explain the decreased e-folding energy of precipitated microbursts compared to that of trapped electrons.

  18. Development of a Short Form of the Boston Naming Test for Individuals with Aphasia

    Science.gov (United States)

    del Toro, Christina M.; Bislick, Lauren P.; Comer, Matthew; Velozo, Craig; Romero, Sergio; Rothi, Leslie J. Gonzalez; Kendall, Diane L.

    2011-01-01

    Purpose: The purpose of this study was to develop a short form of the Boston Naming Test (BNT; Kaplan, Goodglass, & Weintraub, 2001) for individuals with aphasia and compare it with 2 existing short forms originally analyzed with responses from people with dementia and neurologically healthy adults. Method: Development of the new BNT-Aphasia Short…

  19. Thirteen years test experience with short-circuit withstand capability of large power transformers

    NARCIS (Netherlands)

    Smeets, R.P.P.; Paske, te L.H.; Leufkens, P.P.; Fogelberg, T.

    2009-01-01

    The ability to withstand a short circuit is recognised more and more as an essential characteristic of power transformers. IEC and IEEE Standards, as well as other national standards specify short-circuit testing and how to check the withstand capability. Unfortunately, however, there is extensive

  20. Revision to dedicated short range communication roadside equipment specification - RSU 4.1.Bench Test Plan.

    Science.gov (United States)

    2017-04-28

    The document describes the overall process for evaluating Dedicated Short Range Communication (DSRC) Roadside Units (RSU) against USDOT RSU Specification 4.1 in preparation for field evaluation. The Test Cases contained in this document only evaluate...

  1. Amsterdam Short-Term Memory test: a new procedure for the detection of feigned memory deficits

    NARCIS (Netherlands)

    Schagen, S.; Schmand, B.; de Sterke, S.; Lindeboom, J.

    1997-01-01

    The validity of two malingering tests, the newly developed Amsterdam Short-Term Memory (ASTM) test and the Distraction test (Baker, Hanley, Jackson, Kimmance, & Slade, 1993) was examined in a group of patients with closed-head injury (CHI), a normal control group, and a control group with

  2. Within-day variability on short and long walking tests in persons with multiple sclerosis

    NARCIS (Netherlands)

    Feys, P.; Bibby, B.; Romberg, A.; Santoyo, C.; Gebara, B.; de Noordhout, B.M.; Knuts, K.; Bethoux, F.; Skjerbaek, A.; Jensen, E.; Baert, I.; Vaney, C.; de Groot, V.; Dalgas, U.

    2014-01-01

    Objective To compare within-day variability of short (10 m walking test at usual and fastest speed; 10MWT) and long (2 and 6-minute walking test; 2MWT/6MWT) tests in persons with multiple sclerosis. Design Observational study. Setting MS rehabilitation and research centers in Europe and US within

  3. Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy.

    Science.gov (United States)

    Domann, Eugen; Fischer, Florence; Glowatzki, Fabian; Fritzenwanker, Moritz; Hain, Torsten; Zechel-Gran, Silke; Giffhorn-Katz, Susanne; Neubauer, Bernd A

    2016-07-28

    d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic acid bacteria is a rarely diagnosed neurological complication of patients with short bowel syndrome. Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d-lactic acidosis/encephalopathy. Copyright © 2016 Domann et al.

  4. Testing optimization sequence for the beam port facility of PSBR

    International Nuclear Information System (INIS)

    Bekar, K.B.; Azmy, Y.Y.; Unlu, K.

    2005-01-01

    We present preliminary testing results of the modular code package prepared for the size and shape optimization of the beam tube device of the beam port facility at the Penn State Breazeale Reactor (PSBR). In the test cases, using the Min-max algorithm as an optimizer and multidimensional, neutral particle transport code TORT as a transport solver in the physics calculation, we optimize the shape of the D 2 O moderator of the beam tube device. We illustrate the modular nature of the optimization package, validation tests of the physics model, and preliminary optimization calculation via the whole code package. Results obtained so far indicate the drum-shaped D 2 O moderator tank is over-designed in size and does not possess the almost hemi-spherical optimal shape computed by our new package. (authors)

  5. Foreshock sequences and short-term earthquake predictability on East Pacific Rise transform faults.

    Science.gov (United States)

    McGuire, Jeffrey J; Boettcher, Margaret S; Jordan, Thomas H

    2005-03-24

    East Pacific Rise transform faults are characterized by high slip rates (more than ten centimetres a year), predominantly aseismic slip and maximum earthquake magnitudes of about 6.5. Using recordings from a hydroacoustic array deployed by the National Oceanic and Atmospheric Administration, we show here that East Pacific Rise transform faults also have a low number of aftershocks and high foreshock rates compared to continental strike-slip faults. The high ratio of foreshocks to aftershocks implies that such transform-fault seismicity cannot be explained by seismic triggering models in which there is no fundamental distinction between foreshocks, mainshocks and aftershocks. The foreshock sequences on East Pacific Rise transform faults can be used to predict (retrospectively) earthquakes of magnitude 5.4 or greater, in narrow spatial and temporal windows and with a high probability gain. The predictability of such transform earthquakes is consistent with a model in which slow slip transients trigger earthquakes, enrich their low-frequency radiation and accommodate much of the aseismic plate motion.

  6. VARIOUS SPEECH SEQUENCES OF ENGLISH DEPARTMENT STUDENTS IN DOING REQUEST VIA SHORT MESSAGE SERVICE

    Directory of Open Access Journals (Sweden)

    Ike Revita

    2015-09-01

    Full Text Available Interaction, if not wisely considered, may be very risky. The unwise utterances may lead to misunderstanding. When this happens, pragmatic failure is of great possibility occur. This writing is aimed at describing the some variations of speech seqeunces in doing request and the reasons of using each variation. The data are the request uttered by English Department students Andalas University to their friends, their lecturer and vice versa at the campus. Data are collected by observational method, interviewing and note-taking technique. To analyze the data, pragmatic and referential identity method is used. The result of analysis is naratively and descriptively presented. Having been related to the concept of speech act of request (Revita, 2008 and context (Yule, 1986, it is found that there are four variations of speech sequence when English Department students do request. They are (a (1 1 in 1; (b 2 in 1; (c 3 in 1; and (d multi acts in 1. The choice of these variations is basically based on several reasons, namely (i social; (iipsychological; (iii cultural ; and (iv religious aspect.

  7. Change detection in a short time sequence of polarimetric C-band SAR data

    DEFF Research Database (Denmark)

    Nielsen, Allan Aasbjerg; Conradsen, Knut; Skriver, Henning

    2016-01-01

    in the covariance matrix representation is carried out. The omnibus test statistic and its factorization detect if and when change(s) occur. The technique is demonstrated on airborne EMISAR C-band data but may be applied to ALOS, COSMO-SkyMed, RadarSat-2 Sentinel-1, TerraSAR-X, and Yaogan data also....

  8. Seismically induced accident sequence analysis of the advanced test reactor

    International Nuclear Information System (INIS)

    Khericha, S.T.; Henry, D.M.; Ravindra, M.K.; Hashimoto, P.S.; Griffin, M.J.; Tong, W.H.; Nafday, A.M.

    1991-01-01

    A seismic probabilistic risk assessment (PRA) was performed for the Department of Energy (DOE) Advanced Test Reactor (ATR) as part of the external events analysis. The risk from seismic events to the fuel in the core and in the fuel storage canal was evaluated. The key elements of this paper are the integration of seismically induced internal flood and internal fire, and the modeling of human error rates as a function of the magnitude of earthquake. The systems analysis was performed by EG ampersand G Idaho, Inc. and the fragility analysis and quantification were performed by EQE International, Inc. (EQE)

  9. Long-term earthquake forecasts based on the epidemic-type aftershock sequence (ETAS model for short-term clustering

    Directory of Open Access Journals (Sweden)

    Jiancang Zhuang

    2012-07-01

    Full Text Available Based on the ETAS (epidemic-type aftershock sequence model, which is used for describing the features of short-term clustering of earthquake occurrence, this paper presents some theories and techniques related to evaluating the probability distribution of the maximum magnitude in a given space-time window, where the Gutenberg-Richter law for earthquake magnitude distribution cannot be directly applied. It is seen that the distribution of the maximum magnitude in a given space-time volume is determined in the longterm by the background seismicity rate and the magnitude distribution of the largest events in each earthquake cluster. The techniques introduced were applied to the seismicity in the Japan region in the period from 1926 to 2009. It was found that the regions most likely to have big earthquakes are along the Tohoku (northeastern Japan Arc and the Kuril Arc, both with much higher probabilities than the offshore Nankai and Tokai regions.

  10. Optimized Environmental Test Sequences to Ensure the Sustainability and Reliability of Marine Weapons

    Directory of Open Access Journals (Sweden)

    Jung Ho Yang

    2014-11-01

    Full Text Available In recent years, there has been an increase in the types of marine weapons used in response to diverse hostile threats. However, because marine weapons are only tested under a single set of environmental conditions, failures due to different environmental stresses have been difficult to detect. Hence, this study proposes an environmental test sequence for multi-environment testing. The environmental test sequences for electrical units described in the international standard IEC 60068-1, and for military supply described in the United States national standard MIL-STD-810G were investigated to propose guidelines for the appropriate test sequences. This study demonstrated the need for tests in multiple environments by investigating marine weapon accidents, and evaluated which environmental stresses and test items have the largest impacts on marine weapons using a two-phase quality function deployment (QFD analysis of operational scenarios, environmental stresses, and environmental test items. Integer programming was used to determine the most influential test items and the shortest environmental test time, allowing us to propose optimal test procedures. Based on our analysis, we developed optimal environmental test sequences that could be selected by a test designer.

  11. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

    Directory of Open Access Journals (Sweden)

    Hao Ye

    2015-11-01

    Full Text Available Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.

  12. Microstructure and elemental distribution of americium containing MOX fuel under the short term irradiation tests

    International Nuclear Information System (INIS)

    Tanaka, Kosuke; Hirosawa, Takashi; Obayashi, Hiroshi; Koyama, Shin Ichi; Yoshimochi, Hiroshi; Tanaka, Kenya

    2008-01-01

    In order to investigate the effect of americium addition to MOX fuels on the irradiation behavior, the 'Am-1' program is being conducted in JAEA. The Am-1 program consists of two short term irradiation tests of 10-minute and 24 hour irradiations and a steady-state irradiation test. The short-term irradiation tests were successfully completed and the post irradiation examinations (PIEs) are in progress. The PIEs for Am-containing MOX fuels focused on the microstructural evolution and redistribution behavior of Am at the initial stage of irradiation and the results to date are reported

  13. Short term reproducibility of a high contrast 3-D isotropic optic nerve imaging sequence in healthy controls

    Science.gov (United States)

    Harrigan, Robert L.; Smith, Alex K.; Mawn, Louise A.; Smith, Seth A.; Landman, Bennett A.

    2016-03-01

    The optic nerve (ON) plays a crucial role in human vision transporting all visual information from the retina to the brain for higher order processing. There are many diseases that affect the ON structure such as optic neuritis, anterior ischemic optic neuropathy and multiple sclerosis. Because the ON is the sole pathway for visual information from the retina to areas of higher level processing, measures of ON damage have been shown to correlate well with visual deficits. Increased intracranial pressure has been shown to correlate with the size of the cerebrospinal fluid (CSF) surrounding the ON. These measures are generally taken at an arbitrary point along the nerve and do not account for changes along the length of the ON. We propose a high contrast and high-resolution 3-D acquired isotropic imaging sequence optimized for ON imaging. We have acquired scan-rescan data using the optimized sequence and a current standard of care protocol for 10 subjects. We show that this sequence has superior contrast-to-noise ratio to the current standard of care while achieving a factor of 11 higher resolution. We apply a previously published automatic pipeline to segment the ON and CSF sheath and measure the size of each individually. We show that these measures of ON size have lower short- term reproducibility than the population variance and the variability along the length of the nerve. We find that the proposed imaging protocol is (1) useful in detecting population differences and local changes and (2) a promising tool for investigating biomarkers related to structural changes of the ON.

  14. The first DC performance test and analysis of CC conductor short sample at ASIPP conductor test facility

    International Nuclear Information System (INIS)

    Shi Yi; Wu Yu; Liu Huajun; Long Feng; Qian Li; Ren Zhibin; Li Shaolei; Liu Bo; Chen Jinglin

    2012-01-01

    Highlights: ► In this study the first DC performance experiments of ITER correction coil conductor short sample have been carried out in ASIPP test facility. ► A CC conductor short sample was fabricated and tested to confirm the capability of this test facility for qualification tests of CC conductors. ► There is no obvious impact of cycling on DC performance measurement. ► Those measured results of current sharing temperature are in agreement with the expected results from strand scaling - Abstract: The first DC performance experiments of ITER correction coil (CC) conductor short sample have been carried out in the conductor test facility of Institute of Plasma Physics, CAS (ASIPP) in January this year. Those experiments aim to investigate the DC performance of ITER CC conductor. The tested conductor short sample is bended as a half circle with the diameter of 270 mm to meet the background magnetic field shape. The half circle part of sample is longer than the final twist pitch. The current sharing temperature (T cs ) in the 3.86 T external magnetic field (B ex ), ≤12 kA could be measured including the critical current (I c ) run. There is no obvious impact of 1000 cycles on DC performance. Those measured T cs results are in agreement with the expected results from strand scaling.

  15. The sensitivity testing of Wilms' tumors to cytostatic agents with an autoradiographic in vitro short-term test

    International Nuclear Information System (INIS)

    Willnow, U.

    1984-01-01

    Sensitivity of 15 Wilms' tumors in children was tested towards cytostatic agents in vitro by means of an autoradiographic short-term test. Sensitivity was measured as the magnitude of the inhibition of 3 H-thymidine or 3 H-uridine incorporation. The test was performed with Adriamycin, Actinomycin D, Daunomycin, Bleomycin, Cyclophosphamide, Ifosfamide, Trenimon, and Arabinosylcytosine. None of the tumors is resistant to all substances, they are responsive against 2 or more drugs. The most effective drugs tested are Adriamycin, Actinomycin D and Cyclophosphamide. The tumors show a marked individual sensitivity pattern. This behavior is explained mainly by the usually high proliferative activity of Wilms' tumors. The possibilities and limits of long-term and short-term methods for sensitivity testing are discussed critically. For the evaluation of the results of in vitro testing and in vivo effectiveness the close correlation should be considered between the type of cytostatic agent and proliferation kinetics of the tumor, cytostatic agent and effect on tumor metabolism as well as the effect of the cytostatics and the nucleic acid precursors used for the short-term test. Despite the methodological limitations preclinical testing should be preferred to unselected chemotherapy. (author)

  16. An investigation of the genetic toxicology of irradiated foodstuffs using short-term test systems

    International Nuclear Information System (INIS)

    Phillips, B.J.; Kranz, E.; Elias, P.S.

    1980-01-01

    As part of a programme of short-term tests used to detect possible genetic toxicity in irradiated foodstuffs, cultured Chinese hamster ovary cells were exposed to extracts and digests of irradiated and unirradiated dates, fish and chicken and subjected to tests for cytotoxicity, sister chromatid exchange induction and mutation to thioguanine resistance. The results showed no evidence of genetic toxicity induced in food by irradiation. The general applicability of cell culture tests to the detection of mutagens in food is discussed. (author)

  17. Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

    Directory of Open Access Journals (Sweden)

    Myco Umemura

    Full Text Available The development of next-generation sequencing (NGS technologies has dramatically increased the throughput, speed, and efficiency of genome sequencing. The short read data generated from NGS platforms, such as SOLiD and Illumina, are quite useful for mapping analysis. However, the SOLiD read data with lengths of <60 bp have been considered to be too short for de novo genome sequencing. Here, to investigate whether de novo sequencing of fungal genomes is possible using only SOLiD short read sequence data, we performed de novo assembly of the Aspergillus oryzae RIB40 genome using only SOLiD read data of 50 bp generated from mate-paired libraries with 2.8- or 1.9-kb insert sizes. The assembled scaffolds showed an N50 value of 1.6 Mb, a 22-fold increase than those obtained using only SOLiD short read in other published reports. In addition, almost 99% of the reference genome was accurately aligned by the assembled scaffold fragments in long lengths. The sequences of secondary metabolite biosynthetic genes and clusters, whose products are of considerable interest in fungal studies due to their potential medicinal, agricultural, and cosmetic properties, were also highly reconstructed in the assembled scaffolds. Based on these findings, we concluded that de novo genome sequencing using only SOLiD short reads is feasible and practical for molecular biological study of fungi. We also investigated the effect of filtering low quality data, library insert size, and k-mer size on the assembly performance, and recommend for the assembly use of mild filtered read data where the N50 was not so degraded and the library has an insert size of ∼2.0 kb, and k-mer size 33.

  18. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled...... sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  19. Evaluation of short repetition time, partial flip angle, gradient recalled echo pulse sequences in cervical spine imaging

    International Nuclear Information System (INIS)

    Enzmann, D.; Rubin, J.B.

    1987-01-01

    A short repetition time (TR), partial flip angle, gradient recalled echo pulse sequence (GRASS) was prospectively studied to optimize it for the diagnosis of cervical disk and cord disease in 98 patients. Changes in signal-to-noise ratio (SNR) and contrast were measured as the following parameters were varied: flip angle (3 0 to 18 0 ), TR (22-60 msec), and echo time (TE) (12.5-25 msec). Flip angle was the single most important parameter. For disk disease, cerebrospinal fluid (CSF) SNR peaked at an 8 0 flip angle in the axial view but at a 4 0 flip angle in the sagittal view. In the sagittal view, disk-CSF contrast decreased progressively from a flip angle of 3 0 , while in the axial view it peaked at 10 0 . For cord lesions the findings were similar except that lesion-cord contrast could be increased by lengthening both TR and TE. No one combination of parameters proved greatly superior for either disk disease or cord disease. The selection of parameters required balancing of several factors that often had opposing effects

  20. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.

    Science.gov (United States)

    Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D; Proudfoot, Michael; Makarova, Kira S; Kudritska, Marina; Kochinyan, Samvel; Wang, Shuren; Chruszcz, Maksymilian; Minor, Wladek; Koonin, Eugene V; Edwards, Aled M; Savchenko, Alexei; Yakunin, Alexander F

    2008-07-18

    Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.

  1. Device for testing continuity and/or short circuits in a cable

    Science.gov (United States)

    Hayhurst, Arthur R. (Inventor)

    1995-01-01

    A device for testing current paths is attachable to a conductor. The device automatically checks the current paths of the conductor for continuity of a center conductor, continuity of a shield and a short circuit between the shield and the center conductor. The device includes a pair of connectors and a circuit to provide for testing of the conductive paths of the cable. The pair of connectors electrically connects the conductive paths of a cable to be tested with the circuit paths of the circuit. The circuit paths in the circuit include indicators to simultaneously indicate the results of the testing.

  2. Reliability of the Test of Wheeled Mobility (TOWM) and the Short Wheelie Test

    NARCIS (Netherlands)

    Fliess-Douer, Osnat; Van der Woude, Lucas H. V.; Vanlandewijck, Yves C.

    Objective: To assess the reliability of the Test of Wheeled Mobility (TOWM) and the Wheelie test. Design: Cohort study. Setting: Gymnasium. Participants: Manual wheelchair users (N=30, age 23-53y) with a spinal cord injury. Intervention: Participants performed the 30 skills of the TOWM and the 8

  3. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

    Science.gov (United States)

    Schlaberg, Robert; Chiu, Charles Y; Miller, Steve; Procop, Gary W; Weinstock, George

    2017-06-01

    - Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.

  4. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Sakakibara, Yasumbumi

    2011-10-13

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  5. Recurrent plot analysis of discharge sequences in tracking test of polybutylene polymers

    Energy Technology Data Exchange (ETDEWEB)

    Du, B X; Gu, L; Dong, D S [Key Laboratory of Power System Simulation and Control of Ministry of Education, Department of Electrical Engineering, School of Electrical Engineering and Automation, Tianjin University, Tianjin 300072 (China); Zheng, X L [Henan Electric Power Survey and Design Institute, Henan 450007 (China)], E-mail: duboxue@tju.edu.cn

    2008-10-07

    Polymers are required to use in radiation environments as insulation materials. However, they often suffer from tracking failure. There is an increasing demand to evaluate radiation effects on dielectric performance. This paper presents a recurrence plot (RP) approach to analyse surface discharge sequences of gamma-ray irradiated polymer materials based on tracking test. Studying the non-linear characteristics of discharge sequences can assist in understanding the underlying mechanism of the discharge process. Discharge sequences of the test are extended to m-dimensional phase space by using the phase space reconstructed method. As test samples, polybutylene terephthalate (PBT) and polybutylene naphthalate (PBN) were irradiated to 100 kGy and then up to 1 MGy with a dosage rate of 10 kGy h{sup -1} by using a {sup 60}Co gamma source. The tracking tests were carried out according to the test method described in IEC60112. It is found that the RPs can give visual recurrent patterns of discharge sequences for identification of the effects of gamma-ray radiation dosage on the resistance to tracking of the polymers. The detection of recurrent patterns together with comparative tracking index value results indicate that with the increase in the radiation dosage, the resistance to tracking of PBT decreases, but increases for PBN.

  6. Sequence Design for a Test Tube of Interacting Nucleic Acid Strands.

    Science.gov (United States)

    Wolfe, Brian R; Pierce, Niles A

    2015-10-16

    We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

  7. Effect of stereochemistry, chain length and sequence pattern on antimicrobial properties of short synthetic β-sheet forming peptide amphiphiles.

    Science.gov (United States)

    Ong, Zhan Yuin; Cheng, Junchi; Huang, Yuan; Xu, Kaijin; Ji, Zhongkang; Fan, Weimin; Yang, Yi Yan

    2014-01-01

    In the face of mounting global antibiotics resistance, the identification and development of membrane-active antimicrobial peptides (AMPs) as an alternative class of antimicrobial agent have gained significant attention. The physical perturbation and disruption of microbial membranes by the AMPs have been proposed to be an effective means to overcome conventional mechanisms of drug resistance. Recently, we have reported the design of a series of short synthetic β-sheet folding peptide amphiphiles comprised of recurring (X1Y1X2Y2)n-NH2 sequences where X: hydrophobic amino acids, Y: cationic amino acids and n: number of repeat units. In efforts to investigate the effects of key parameters including stereochemistry, chain length and sequence pattern on antimicrobial effects, systematic d-amino acid substitutions of the lead peptides (IRIK)2-NH2 (IK8-all L) and (IRVK)3-NH2 (IK12-all L) were performed. It was found that the corresponding D-enantiomers exhibited stronger antimicrobial activities with minimal or no change in hemolytic activities, hence translating very high selectivity indices of 407.0 and >9.8 for IK8-all D and IK12-all D respectively. IK8-all D was also demonstrated to be stable to degradation by broad spectrum proteases trypsin and proteinase K. The membrane disrupting bactericidal properties of IK8-all D effectively prevented drug resistance development and inhibited the growth of various clinically isolated MRSA, VRE, Acinetobacter baumanni, Pseudomonas aeruginosa, Cryptococcus. neoformans and Mycobacterium tuberculosis. Significant reduction in intracellular bacteria counts was also observed following treatment with IK8-all D in the Staphylococcus. aureus infected mouse macrophage cell line RAW264.7 (P < 0.01). These results suggest that the d-amino acids substituted β-sheet forming peptide IK8-all D with its enhanced antimicrobial activities and improved protease stability, is a promising therapeutic candidate with potential to combat

  8. 40 CFR Table C-2 to Subpart C of... - Sequence of Test Measurements

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Sequence of Test Measurements C Table C-2 to Subpart C of Part 53 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Medium. 2 High High. 3 Medium Low. 4 High High. 5 Low Medium. 6 Medium Low. 7 Low Medium. 8 Medium Low. 9...

  9. Genetic counselors’ (GC) knowledge, awareness, and understanding of clinical next-generation sequencing (NGS) genomic testing

    Science.gov (United States)

    Boland, PM; Ruth, K; Matro, JM; Rainey, KL; Fang, CY; Wong, YN; Daly, MB; Hall, MJ

    2014-01-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation. PMID:25523111

  10. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    Science.gov (United States)

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. X-ray testing for short-time dynamic applications; Roentgenuntersuchungen fuer kurzzeitdynamische Anwendungen

    Energy Technology Data Exchange (ETDEWEB)

    Kurfiss, Malte; Moser, Stefan; Popko, Gregor; Nau, Siegfried [Fraunhofer-Institut fuer Kurzzeitdynamik, Efringen-Kirchen (Germany). Ernst-Mach-Inst. (EMI)

    2017-08-01

    For nondestructive testing purposes new challenges are short-time dynamic processes. The application of x-ray flash tubes and modern high-speed cameras allows the observation of the opening of air-bags or the energy absorption of compressed tubes as occurring during a vehicle crash. Special algorithms designed for computerized tomography analyses allow the 3D reconstruction at individual time points of the dynamic process. Possibilities and limitations of the actual techniques are discussed.

  12. Mercury Induced Biochemical Alterations As Oxidative Stress In Mugil Cephalus In Short Term Toxicity Test

    OpenAIRE

    J.S.I Rajkumar; Samuel Tennyson

    2013-01-01

    Mugil cephalus juveniles of size 2.5 ±0.6cm were exposed to mercury in short term chronic toxicity test through static renewal bioassay to detect the possible biochemical agent as biomarkers in aquatic pollution and in estuarine contamination as specific. Lipid peroxidation levels, glutathione S -transferase, catalase, reduced glutathione and acetylcholinesterase were studied as biochemical parameters. Increased thio-barbituric acid reactive substances levels were observed under exposur...

  13. Fundamental tests and measures of the structure of matter at short distances

    International Nuclear Information System (INIS)

    Brodsky, S.J.

    1981-07-01

    Recent progress in gauge field theories has led to a new perspective on the structure of matter and basic interactions at short distances. It is clear that at very high energies quantum electrodynamics, together with the weak and strong interactions, are part of a unified theory with new fundamental constants, new symmetries, and new conservation laws. A non-technical introduction to these topics is given, with emphasis on fundamental tests and measurements. 21 references

  14. Reliability testing of the Danish version of the Kidney Disease Quality of Life Short Form

    DEFF Research Database (Denmark)

    Molsted, Stig; Heaf, James; Prescott, Lotte

    2005-01-01

    . MATERIAL AND METHODS: Translation into Danish and back-translation into English were performed. Pilot, field and internal consistency reliability tests were performed. RESULTS: Cronbach's alpha coefficients for the internal reliability test ranged from 0.77 to 0.93 for the eight generic scales. In a test......OBJECTIVE: The questionnaire Kidney Disease Quality of Life Short Form version 1.3 (KDQOL-SF) is valuable for assessing the health-related quality of life in patients treated with chronic dialysis. The aim of this study was to translate and test the reliability of the KDQOL-SF for use in Denmark...... involving all patients, two of the disease-specific scales had Cronbach's alpha coefficients of test of the scores...

  15. Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine.

    Science.gov (United States)

    Ji, Yuan; Si, Yue; McMillin, Gwendolyn A; Lyon, Elaine

    2018-04-23

    The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

  16. Association testing for next-generation sequencing data using score statistics

    DEFF Research Database (Denmark)

    Skotte, Line; Korneliussen, Thorfinn Sand; Albrechtsen, Anders

    2012-01-01

    computationally feasible due to the use of score statistics. As part of the joint likelihood, we model the distribution of the phenotypes using a generalized linear model framework, which works for both quantitative and discrete phenotypes. Thus, the method presented here is applicable to case-control studies...... of genotype calls into account have been proposed; most require numerical optimization which for large-scale data is not always computationally feasible. We show that using a score statistic for the joint likelihood of observed phenotypes and observed sequencing data provides an attractive approach...... to association testing for next-generation sequencing data. The joint model accounts for the genotype classification uncertainty via the posterior probabilities of the genotypes given the observed sequencing data, which gives the approach higher power than methods based on called genotypes. This strategy remains...

  17. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

    Directory of Open Access Journals (Sweden)

    Thiele Bernhard

    2011-05-01

    Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

  18. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

    Science.gov (United States)

    Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

    2011-05-13

    Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

  19. Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT).

    Science.gov (United States)

    Urrutia, Eugene; Lee, Seunggeun; Maity, Arnab; Zhao, Ni; Shen, Judong; Li, Yun; Wu, Michael C

    Analysis of rare genetic variants has focused on region-based analysis wherein a subset of the variants within a genomic region is tested for association with a complex trait. Two important practical challenges have emerged. First, it is difficult to choose which test to use. Second, it is unclear which group of variants within a region should be tested. Both depend on the unknown true state of nature. Therefore, we develop the Multi-Kernel SKAT (MK-SKAT) which tests across a range of rare variant tests and groupings. Specifically, we demonstrate that several popular rare variant tests are special cases of the sequence kernel association test which compares pair-wise similarity in trait value to similarity in the rare variant genotypes between subjects as measured through a kernel function. Choosing a particular test is equivalent to choosing a kernel. Similarly, choosing which group of variants to test also reduces to choosing a kernel. Thus, MK-SKAT uses perturbation to test across a range of kernels. Simulations and real data analyses show that our framework controls type I error while maintaining high power across settings: MK-SKAT loses power when compared to the kernel for a particular scenario but has much greater power than poor choices.

  20. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq

    Directory of Open Access Journals (Sweden)

    Manabu Nakayama

    2017-03-01

    Full Text Available Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA, also known as neonatal-onset multisystem inflammatory disease (NOMID. In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses. To increase the availability of such testing, low-cost high-throughput gene-analysis systems are required, ones that not only have the sensitivity to detect even low-level somatic mosaic mutations, but also can operate simply in a clinical setting. To this end, we developed a simple method that employs two-step tailed PCR and an NGS system, MiSeq platform, to detect mutations in all coding exons of the 12 genes responsible for autoinflammatory diseases. Using this amplicon sequencing system, we amplified a total of 234 amplicons derived from the 12 genes with multiplex PCR. This was done simultaneously and in one test tube. Each sample was distinguished by an index sequence of second PCR primers following PCR amplification. With our procedure and tips for reducing PCR amplification bias, we were able to analyze 12 genes from 25 clinical samples in one MiSeq run. Moreover, with the certified primers designed by our short program—which detects and avoids common SNPs in gene-specific PCR primers—we used this system for routine genetic testing. Our optimized procedure uses a simple protocol, which can easily be followed by virtually any office medical staff. Because of the small PCR amplification bias, we can analyze simultaneously several clinical DNA samples with low cost and can obtain sufficient read numbers to detect a low level of

  1. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq.

    Science.gov (United States)

    Nakayama, Manabu; Oda, Hirotsugu; Nakagawa, Kenji; Yasumi, Takahiro; Kawai, Tomoki; Izawa, Kazushi; Nishikomori, Ryuta; Heike, Toshio; Ohara, Osamu

    2017-03-01

    Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA), also known as neonatal-onset multisystem inflammatory disease (NOMID). In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses. To increase the availability of such testing, low-cost high-throughput gene-analysis systems are required, ones that not only have the sensitivity to detect even low-level somatic mosaic mutations, but also can operate simply in a clinical setting. To this end, we developed a simple method that employs two-step tailed PCR and an NGS system, MiSeq platform, to detect mutations in all coding exons of the 12 genes responsible for autoinflammatory diseases. Using this amplicon sequencing system, we amplified a total of 234 amplicons derived from the 12 genes with multiplex PCR. This was done simultaneously and in one test tube. Each sample was distinguished by an index sequence of second PCR primers following PCR amplification. With our procedure and tips for reducing PCR amplification bias, we were able to analyze 12 genes from 25 clinical samples in one MiSeq run. Moreover, with the certified primers designed by our short program-which detects and avoids common SNPs in gene-specific PCR primers-we used this system for routine genetic testing. Our optimized procedure uses a simple protocol, which can easily be followed by virtually any office medical staff. Because of the small PCR amplification bias, we can analyze simultaneously several clinical DNA samples with low cost and can obtain sufficient read numbers to detect a low level of somatic mosaic mutations.

  2. Psychometric testing of the properties of the spiritual health scale short form.

    Science.gov (United States)

    Hsiao, Ya-Chu; Chiang, Yi-Chien; Lee, Hsiang-Chun; Han, Chin-Yen

    2013-11-01

    To further examine the psychometric properties of the spiritual health scale short form, including its reliability and validity. Spirituality is one of the main factors associated with good health outcomes. A reliable and valid instrument to measure spirituality is essential to identify the spiritual needs of an individual and to evaluate the effect of spiritual care. A cross-sectional study design was used. The study was conducted in six nursing schools in northern, central and southern Taiwan. The inclusion criterion for participants was nursing students with clinical practice experience. Initially, 1141 participants were recruited for the study, but 67 were absent and 48 did not complete the questionnaires. A total of 1026 participants were finally recruited, indicating a response rate of 89·9%. The psychometric testing of the spiritual health scale short form included construct validity with confirmatory factor analysis, known-group validity and internal consistency reliability. The results of the confirmatory factor analysis supported the five-factor model as an acceptable model fit. In the known-group validity, the results indicated that people who are in the category of primary religious affiliation have better spiritual health than people in the category of secondary religious affiliation and atheism. The result also indicated that the 24-item spiritual health scale short form achieved an acceptable internal consistency coefficient. The findings suggest that the spiritual health scale short form is a valid and reliable instrument for the appraisal of individual spiritual health. The spiritual health scale short form could provide useful information to guide clinical practice in assessing and managing people's spiritual health in Taiwan. © 2013 John Wiley & Sons Ltd.

  3. 40 CFR 1065.935 - Emission test sequence for field testing.

    Science.gov (United States)

    2010-07-01

    ... value for the previous 2 min or until an engine thermostat controls engine temperature with coolant or... media, such as evacuated bags or tare-weighed PM sample media. (2) Operate the PEMS according to the... ambient data, and integrate measured values using a PEMS. (3) If engine starting is part of field testing...

  4. Modified SPC for short run test and measurement process in multi-stations

    Science.gov (United States)

    Koh, C. K.; Chin, J. F.; Kamaruddin, S.

    2018-03-01

    Due to short production runs and measurement error inherent in electronic test and measurement (T&M) processes, continuous quality monitoring through real-time statistical process control (SPC) is challenging. Industry practice allows the installation of guard band using measurement uncertainty to reduce the width of acceptance limit, as an indirect way to compensate the measurement errors. This paper presents a new SPC model combining modified guard band and control charts (\\bar{\\text{Z}} chart and W chart) for short runs in T&M process in multi-stations. The proposed model standardizes the observed value with measurement target (T) and rationed measurement uncertainty (U). S-factor (S f) is introduced to the control limits to improve the sensitivity in detecting small shifts. The model was embedded in automated quality control system and verified with a case study in real industry.

  5. Within-day variability on short and long walking tests in persons with multiple sclerosis.

    Science.gov (United States)

    Feys, Peter; Bibby, Bo; Romberg, Anders; Santoyo, Carme; Gebara, Benoit; de Noordhout, Benoit Maertens; Knuts, Kathy; Bethoux, Francois; Skjerbæk, Anders; Jensen, Ellen; Baert, Ilse; Vaney, Claude; de Groot, Vincent; Dalgas, Ulrik

    2014-03-15

    To compare within-day variability of short (10 m walking test at usual and fastest speed; 10MWT) and long (2 and 6-minute walking test; 2MWT/6MWT) tests in persons with multiple sclerosis. Observational study. MS rehabilitation and research centers in Europe and US within RIMS (European network for best practice and research in MS rehabilitation). Ambulatory persons with MS (Expanded Disability Status Scale 0-6.5). Subjects of different centers performed walking tests at 3 time points during a single day. 10MWT, 2MWT and 6MWT at fastest speed and 10MWT at usual speed. Ninety-five percent limits of agreement were computed using a random effects model with individual pwMS as random effect. Following this model, retest scores are with 95% certainty within these limits of baseline scores. In 102 subjects, within-day variability was constant in absolute units for the 10MWT, 2MWT and 6MWT at fastest speed (+/-0.26, 0.16 and 0.15m/s respectively, corresponding to +/-19.2m and +/-54 m for the 2MWT and 6MWT) independent on the severity of ambulatory dysfunction. This implies a greater relative variability with increasing disability level, often above 20% depending on the applied test. The relative within-day variability of the 10MWT at usual speed was +/-31% independent of ambulatory function. Absolute values of within-day variability on walking tests at fastest speed were independent of disability level and greater with short compared to long walking tests. Relative within-day variability remained overall constant when measured at usual speed. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  6. GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing

    Directory of Open Access Journals (Sweden)

    Yu GongXin

    2010-10-01

    Full Text Available Abstract Background Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions with multiple variants of genes in the bacterial population, and variations that occur in large gene families. GenHtr accomplishes this by building and comparatively analyzing genome-wide heterogeneity genotypes for both the newly sequenced genomes (using massive short-read sequencing and their isogenic reference (using simulated data. As proof of the concept, this approach was applied to SRX007711, the Solexa sequencing data for a newly sequenced Staphylococcus aureus subsp. USA300 cell line, and demonstrated that it could predict such multiple variants. They include multiple variants of genes critical in pathogenesis, e.g. genes encoding a LysR family transcriptional regulator, 23 S ribosomal RNA, and DNA mismatch repair protein MutS. The heterogeneity results in non-synonymous and nonsense mutations, leading to truncated proteins for both LysR and MutS. Conclusion GenHtr was developed for genome-wide heterogeneity analysis. Although it is much more time

  7. Engineering scale tests of mechanical disassembly and short stroke shearing systems for FBR fuel assembly

    International Nuclear Information System (INIS)

    Higuchi, Hidetoshi; Kitagaki, Toru; Koizumi, Kenji; Hirano, Hiroyasu; Takeuchi, Masayuki; Washiya, Tadahiro; Kawabe, Yukinari; Kobayashi, Tsuguyuki

    2011-01-01

    Japan Atomic Energy Agency (JAEA) and The Japan Atomic Power Company (JAPC) have been developing an advanced head-end process based on mechanical disassembly and short stroke shearing systems as a part of Fast Reactor Cycle Technology Development (FaCT). Fuel pins for a fast reactor are installed within a hexagonal shaped wrapper tube made of stainless steel. In order to reprocess the fast reactor fuel pins, they must be removed from the wrapper tube and transported to the shearing system without failure. In addition, the advanced aqueous reprocessing process, called 'NEXT' (New Extraction System for TRU Recovery) process requires a solution of the spent fuel with relatively high concentration (500g/L). JAEA and JAPC have developed the mechanical disassembly and the short stroke shearing technology which is expected to make fragmented fuel to satisfy these requirements. This paper reports the results of engineering scale tests on the mechanical disassembly and short stroke shearing systems. These tests were carried out with simulated FBR fuel assembly and removed pins. The mechanical cutting method has been developed to avoid fuel pin failure during disassembly operation. The cutting process is divided into two modes, so called 'slit-cut' for cutting the wrapper tube and 'crop-cut' for the end plug region of the fuel pin bundle. In the slit-cut mode, the depth of cutting was automatically controlled based on the calculated wastage of the cutting tool and deformation of the wrapper tube which had been measured before the cutting. This procedure was confirmed to minimize the fuel pin failure which was hard to prevent in the case of laser cutting. The cutting speed was also controlled automatically by the electric current of the cutting motor to lower the load of the cutting tool. The removed fuel pins were transported to the shearing machine, whose fuel shearing magazine width was set to be narrow to realize the suitable configuration for the short stroke shearing

  8. Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland.

    Science.gov (United States)

    Shilaih, Mohaned; Marzel, Alex; Yang, Wan Lin; Scherrer, Alexandra U; Schüpbach, Jörg; Böni, Jürg; Yerly, Sabine; Hirsch, Hans H; Aubert, Vincent; Cavassini, Matthias; Klimkait, Thomas; Vernazza, Pietro L; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F; Kouyos, Roger

    2016-06-14

    Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8-2.1), female gender (OR: 1.6; 95% CI: 1.4-1.7), black ethnicity (OR: 1.9; 95% CI: 1.7-2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6-2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS'. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance.

  9. Preliminary Validation of a New Measure of Negative Response Bias: The Temporal Memory Sequence Test.

    Science.gov (United States)

    Hegedish, Omer; Kivilis, Naama; Hoofien, Dan

    2015-01-01

    The Temporal Memory Sequence Test (TMST) is a new measure of negative response bias (NRB) that was developed to enrich the forced-choice paradigm. The TMST does not resemble the common structure of forced-choice tests and is presented as a temporal recall memory test. The validation sample consisted of 81 participants: 21 healthy control participants, 20 coached simulators, and 40 patients with acquired brain injury (ABI). The TMST had high reliability and significantly high positive correlations with the Test of Memory Malingering and Word Memory Test effort scales. Moreover, the TMST effort scales exhibited high negative correlations with the Glasgow Coma Scale, thus validating the previously reported association between probable malingering and mild traumatic brain injury. A suggested cutoff score yielded acceptable classification rates in the ABI group as well as in the simulator and control groups. The TMST appears to be a promising measure of NRB detection, with respectable rates of reliability and construct and criterion validity.

  10. Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features

    Directory of Open Access Journals (Sweden)

    Gillet Laurent

    2011-08-01

    Full Text Available Abstract Background Bovine herpesvirus 4 (BoHV-4 is a useful model for the human pathogenic gammaherpesviruses Epstein-Barr virus and Kaposi's Sarcoma-associated Herpesvirus. Although genome manipulations of this virus have been greatly facilitated by the cloning of the BoHV-4 V.test strain as a Bacterial Artificial Chromosome (BAC, the lack of a complete genome sequence for this strain limits its experimental use. Methods In this study, we have determined the complete sequence of BoHV-4 V.test strain by a pyrosequencing approach. Results The long unique coding region (LUR consists of 108,241 bp encoding at least 79 open reading frames and is flanked by several polyrepetitive DNA units (prDNA. As previously suggested, we showed that the prDNA unit located at the left prDNA-LUR junction (prDNA-G differs from the other prDNA units (prDNA-inner. Namely, the prDNA-G unit lacks the conserved pac-2 cleavage and packaging signal in its right terminal region. Based on the mechanisms of cleavage and packaging of herpesvirus genomes, this feature implies that only genomes bearing left and right end prDNA units are encapsulated into virions. Conclusions In this study, we have determined the complete genome sequence of the BAC-cloned BoHV-4 V.test strain and identified genome organization features that could be important in other herpesviruses.

  11. Testing statistical significance scores of sequence comparison methods with structure similarity

    Directory of Open Access Journals (Sweden)

    Leunissen Jack AM

    2006-10-01

    Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

  12. Design and test of a short mockup magnet for the superconducting undulator at the SSRF

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Jieping, E-mail: jpxu@sinap.ac.cn; Ding, Yi; Cui, Jian; Zhang, Wei; Wang, Hongfei; Yin, Lixin [Department of Mechanical Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204 (China)

    2016-07-27

    A superconducting planar undulator is under development at the Shanghai Synchrotron Radiation Facility (SSRF) to provide the SSRF users with higher photon fluxes at higher photon energies. A 5-period magnet was designed and built for feasibility study. The short mockup magnet is composed of NbTi/Cu winding and low carbon steel former and was tested in a vertical cryocooler-cooled cryostat. The nominal current of 387 A was reached after 2 quenches and the maximum current of 433.2 A was achieved. The magnetic field profile was measured and a peak field of 0.93 T was obtained when stably operating at 400 A.

  13. Two-photon collisions and short-distance tests of quantum chromodynamics

    International Nuclear Information System (INIS)

    Brodsky, S.J.

    1978-12-01

    The physics of two-photon collisions in e +- storage rings is reviewed with emphasis on the predictions of perturbative quantum chromodynamics for high transverse momentum reactions. It is noted that because of the remarkable scaling properties predicted by the theory, two-photon collisions may be proved one of the cleanest tests of the quantum chromodynamics picture of short distance hadron dynamics. In order to contrast these predictions for photon-induced reactions with those for incident hadrons, predictions from quantum chromodynamics for hadron structure functions and form factors at large momentum transfer are also discussed. 55 references

  14. A Method to Select Software Test Cases in Consideration of Past Input Sequence

    International Nuclear Information System (INIS)

    Kim, Hee Eun; Kim, Bo Gyung; Kang, Hyun Gook

    2015-01-01

    In the Korea Nuclear I and C Systems (KNICS) project, the software for the fully-digitalized reactor protection system (RPS) was developed under a strict procedure. Even though the behavior of the software is deterministic, the randomness of input sequence produces probabilistic behavior of software. A software failure occurs when some inputs to the software occur and interact with the internal state of the digital system to trigger a fault that was introduced into the software during the software lifecycle. In this paper, the method to select test set for software failure probability estimation is suggested. This test set reflects past input sequence of software, which covers all possible cases. In this study, the method to select test cases for software failure probability quantification was suggested. To obtain profile of paired state variables, relationships of the variables need to be considered. The effect of input from human operator also have to be considered. As an example, test set of PZR-PR-Lo-Trip logic was examined. This method provides framework for selecting test cases of safety-critical software

  15. Is a sequence of tests during urethral pressure profilometry correlated with symptoms assessment in women?

    Science.gov (United States)

    Valentini, Françoise A; Robain, Gilberte; Marti, Brigitte G

    2012-01-01

    Our purpose was, applying a strictly defined protocol for urethral profilometry, 1) to test the repeatability of same session rest maximum urethral closure pressure (MUCP) and 2) to search for correlation between women complaint and the changes in MUCP value (rest and dynamic tests). A population of 140 consecutive women referred for evaluation of lower urinary tract dysfunction was stratified in 4 groups according with the urinary symptoms: stress, urge, mixed incontinence and continent and in each group in 3 age groups (young, middle age and old). The sequence of tests recorded in supine position was: urethral pressure profile at rest bladder empty, after bladder filling at 250 mL (reference test), stress profile, fatigability (before (rest) and after 10 successive strong coughs), then in standing position. In all groups, there was no significant difference between the two MUCP values at rest bladder filled. In the three incontinent groups, MUCP was higher bladder empty than bladder filled (p rest bladder filled has a good repeatability in individual. However a complex sequence of tests during urethral pressure profilometry remains discussed in middle-age and old age-groups, it allows specifying the stress component of incontinence in young women and the urgency component in all age-groups.

  16. Hypothesis testing on the fractal structure of behavioral sequences: the Bayesian assessment of scaling methodology.

    Science.gov (United States)

    Moscoso del Prado Martín, Fermín

    2013-12-01

    I introduce the Bayesian assessment of scaling (BAS), a simple but powerful Bayesian hypothesis contrast methodology that can be used to test hypotheses on the scaling regime exhibited by a sequence of behavioral data. Rather than comparing parametric models, as typically done in previous approaches, the BAS offers a direct, nonparametric way to test whether a time series exhibits fractal scaling. The BAS provides a simpler and faster test than do previous methods, and the code for making the required computations is provided. The method also enables testing of finely specified hypotheses on the scaling indices, something that was not possible with the previously available methods. I then present 4 simulation studies showing that the BAS methodology outperforms the other methods used in the psychological literature. I conclude with a discussion of methodological issues on fractal analyses in experimental psychology. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  17. Humans can consciously generate random number sequences: a possible test for artificial intelligence.

    Science.gov (United States)

    Persaud, Navindra

    2005-01-01

    Computer algorithms can only produce seemingly random or pseudorandom numbers whereas certain natural phenomena, such as the decay of radioactive particles, can be utilized to produce truly random numbers. In this study, the ability of humans to generate random numbers was tested in healthy adults. Subjects were simply asked to generate and dictate random numbers. Generated numbers were tested for uniformity, independence and information density. The results suggest that humans can generate random numbers that are uniformly distributed, independent of one another and unpredictable. If humans can generate sequences of random numbers then neural networks or forms of artificial intelligence, which are purported to function in ways essentially the same as the human brain, should also be able to generate sequences of random numbers. Elucidating the precise mechanism by which humans generate random number sequences and the underlying neural substrates may have implications in the cognitive science of decision-making. It is possible that humans use their random-generating neural machinery to make difficult decisions in which all expected outcomes are similar. It is also possible that certain people, perhaps those with neurological or psychiatric impairments, are less able or unable to generate random numbers. If the random-generating neural machinery is employed in decision making its impairment would have profound implications in matters of agency and free will.

  18. Effects of tonal language background on tests of temporal sequencing in children.

    Science.gov (United States)

    Mukari, Siti Zamratol-Mai S; Yu, Xuan; Ishak, Wan Syafira; Mazlan, Rafidah

    2015-01-01

    The aims of the present study were to determine the effects of language background on the performance of the pitch pattern sequence test (PPST) and duration pattern sequence test (DPST). As temporal order sequencing may be affected by age and working memory, these factors were also studied. Performance of tonal and non-tonal language speakers on PPST and DPST were compared. Twenty-eight native Mandarin (tonal language) speakers and twenty-nine native Malay (non-tonal language) speakers between seven to nine years old participated in this study. The results revealed that relative to native Malay speakers, native Mandarin speakers demonstrated better scores on the PPST in both humming and verbal labeling responses. However, a similar language effect was not apparent in the DPST. An age effect was only significant in the PPST (verbal labeling). Finally, no significant effect of working memory was found on the PPST and the DPST. These findings suggest that the PPST is affected by tonal language background, and highlight the importance of developing different normative values for tonal and non-tonal language speakers.

  19. Effects of acute caffeine withdrawal on Short Category Test performance in sleep-deprived individuals.

    Science.gov (United States)

    Killgore, William D S; Kahn-Greene, Ellen T; Killgore, Desiree B; Kamimori, Gary H; Balkin, Thomas J

    2007-12-01

    Caffeine is a popular stimulant often used to counter the effects of sleep loss and fatigue. Withdrawal from caffeine may produce mild declines in simple cognitive capacities such as attention and concentration, but it is unclear whether more complex cognitive functions, such as abstract reasoning or concept formation, may be similarly affected. To assess the effect of acute caffeine withdrawal on executive functioning during sleep deprivation, 26 healthy volunteers were administered in double-blind form either repeated doses of caffeine or placebo over two nights of continuous wakefulness. The 108-item Short Category Test was administered after 56 hr. of total sleep deprivation (9 hr. post-caffeine administration). The caffeine group scored significantly more poorly, making approximately 57% more errors on the test than the placebo group. These findings suggest that acute caffeine withdrawal during prolonged sleep deprivation has an adverse effect on abstract reasoning and concept formation.

  20. Validity of a new assessment rubric for a short-answer test of clinical reasoning.

    Science.gov (United States)

    Yeung, Euson; Kulasagarem, Kulamakan; Woods, Nicole; Dubrowski, Adam; Hodges, Brian; Carnahan, Heather

    2016-07-26

    The validity of high-stakes decisions derived from assessment results is of primary concern to candidates and certifying institutions in the health professions. In the field of orthopaedic manual physical therapy (OMPT), there is a dearth of documented validity evidence to support the certification process particularly for short-answer tests. To address this need, we examined the internal structure of the Case History Assessment Tool (CHAT); this is a new assessment rubric developed to appraise written responses to a short-answer test of clinical reasoning in post-graduate OMPT certification in Canada. Fourteen physical therapy students (novices) and 16 physical therapists (PT) with minimal and substantial OMPT training respectively completed a mock examination. Four pairs of examiners (n = 8) participated in appraising written responses using the CHAT. We conducted separate generalizability studies (G studies) for all participants and also by level of OMPT training. Internal consistency was calculated for test questions with more than 2 assessment items. Decision studies were also conducted to determine optimal application of the CHAT for OMPT certification. The overall reliability of CHAT scores was found to be moderate; however, reliability estimates for the novice group suggest that the scale was incapable of accommodating for scores of novices. Internal consistency estimates indicate item redundancies for several test questions which will require further investigation. Future validity studies should consider discriminating the clinical reasoning competence of OMPT trainees strictly at the post-graduate level. Although rater variance was low, the large variance attributed to error sources not incorporated in our G studies warrant further investigations into other threats to validity. Future examination of examiner stringency is also warranted.

  1. From psychological need satisfaction to intentional behavior: testing a motivational sequence in two behavioral contexts.

    Science.gov (United States)

    Hagger, Martin S; Chatzisarantis, Nikos L D; Harris, Jemma

    2006-02-01

    The present study tested a motivational sequence in which global-level psychological need satisfaction from self-determination theory influenced intentions and behavior directly and indirectly through contextual-level motivation and situational-level decision-making constructs from the theory of planned behavior. Two samples of university students (N = 511) completed measures of global-level psychological need satisfaction, contextual-level autonomous motivation, and situational-level attitudes, subjective norms, perceived behavioral control, intentions, and behavior in two behavioral contexts: exercise and dieting. A structural equation model supported the proposed sequence in both samples. The indirect effect was present for exercise behavior, whereas both direct and indirect effects were found for dieting behavior. Findings independently supported the component theories and provided a comprehensive integrated explanation of volitional behavior.

  2. Review of short-term screening tests for mutagens, toxigens, and carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Carney, H.J.; Hass, B.S.

    1979-07-01

    In order to test the thousands of man-made chemicals in the environment for carcinogenic and genetic hazards, a multitude of short-term screening tests has been developed to complement long-term mammalian bioassays and epidemiological studies. These tests cover a broad spectrum of organisms, and include the use of naked and viral nucleic acids, bacteria, fungi, higher plants, insects in vitro mammalian cell cultures (cell transformation, cell-mediated mutagenesis, DNA repair, and chromosome aberration tests) and live mammals. Assay end points include effects on nucleic acids, DNA repair synthesis, point or gene mutation, structural and numerical chromosome aberrations, cytological alterations, and in vitro cell transformation. The present review describes and compares these assays. In addition, it discusses their historical development, the problems and limitations associated with their use, and their implementation in comprehensive testing programs. It is intended to provide overview and specific information to the laboratory that is in the process of establishing genetic toxicological systems. (The literature is reviewed to January 1978.)

  3. A non-accelerating foreshock sequence followed by a short period of quiescence for a large inland earthquake

    Science.gov (United States)

    Doi, I.; Kawakata, H.

    2012-12-01

    Laboratory experiments [e.g. Scholz, 1968; Lockner et al., 1992] and field observations [e.g. Dodge et al., 1996; Helmstetter and Sornette, 2003; Bouchon et al., 2011] have elucidated part of foreshock behavior and mechanism, but we cannot identify foreshocks while they are occurring. Recently, in Japan, a dense seismic network, Hi-net (High Sensitivity Seismograph Network), provides continuous waveform records for regional seismic events. The data from this network enable us to analyze small foreshocks which occur on long period time scales prior to a major event. We have an opportunity to grasp the more detailed pattern of foreshock generation. Using continuous waveforms recorded at a seismic station located in close proximity to the epicenter of the 2008 Iwate-Miyagi inland earthquake, we conducted a detailed investigation of its foreshocks. In addition to the two officially recognized foreshocks, calculation of cross-correlation coefficients between the continuous waveform record and one of the previously recognized foreshocks revealed that 20 micro foreshocks occurred within the same general area. Our analysis also shows that all of these foreshocks occurred within the same general area relative to the main event. Over the two week period leading up to the Iwate-Miyagi earthquake, such foreshocks only occurred during the last 45 minutes, specifically over a 35 minute period followed by a 10 minute period of quiescence just before the mainshock. We found no evidence of acceleration of this foreshock sequence. Rock fracturing experiments using a constant loading rate or creep tests have consistently shown that the occurrence rate of small fracturing events (acoustic emissions; AEs) increases before the main rupture [Scholz, 1968]. This accelerative pattern of preceding events was recognized in case of the 1999 Izmit earthquake [Bouchon et al., 2011]. Large earthquakes however need not be accompanied by acceleration of foreshocks if a given fault's host rock

  4. Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

    DEFF Research Database (Denmark)

    Skovgaard, Ole; Bak, Mads; Løbner-Olesen, Anders

    2011-01-01

    a combination of WGS and genome copy number analysis, for the identification of mutations that suppress the growth deficiency imposed by excessive initiations from the Escherichia coli origin of replication, oriC. The E. coli chromosome, like the majority of bacterial chromosomes, is circular, and DNA...... replication is initiated by assembling two replication complexes at the origin, oriC. These complexes then replicate the chromosome bidirectionally toward the terminus, ter. In a population of growing cells, this results in a copy number gradient, so that origin-proximal sequences are more frequent than...... origin-distal sequences. Major rearrangements in the chromosome are, therefore, readily identified by changes in copy number, i.e., certain sequences become over- or under-represented. Of the eight mutations analyzed in detail here, six were found to affect a single gene only, one was a large chromosomal...

  5. Is a sequence of tests during urethral pressure profilometry correlated with symptoms assessment in women?

    Directory of Open Access Journals (Sweden)

    Françoise A. Valentini

    2012-12-01

    Full Text Available Introduction Our purpose was, applying a strictly defined protocol for urethral profilometry, 1 to test the repeatability of same session rest maximum urethral closure pressure (MUCP and 2 to search for correlation between women complaint and the changes in MUCP value (rest and dynamic tests. Materials and Methods A population of 140 consecutive women referred for evaluation of lower urinary tract dysfunction was stratified in 4 groups according with the urinary symptoms: stress, urge, mixed incontinence and continent and in each group in 3 age groups (young, middle age and old. The sequence of tests recorded in supine position was: urethral pressure profile at rest bladder empty, after bladder filling at 250 mL (reference test, stress profile, fatigability (before (rest and after 10 successive strong coughs, then in standing position. Results In all groups, there was no significant difference between the two MUCP values at rest bladder filled. In the three incontinent groups, MUCP was higher bladder empty than bladder filled (p < 0.05 except in the young sub-group. Stress incontinence led to significant decrease of MUCP during dynamic tests in the young group. MUCP was not modified after fatigability test in women with urge complaint whatever age. Conclusion When recorded following a strictly defined protocol, MUCP at rest bladder filled has a good repeatability in individual. However a complex sequence of tests during urethral pressure profilometry remains discussed in middle-age and old age-groups, it allows specifying the stress component of incontinence in young women and the urgency component in all age-groups.

  6. Empirical versus Random Item Selection in the Design of Intelligence Test Short Forms--The WISC-R Example.

    Science.gov (United States)

    Goh, David S.

    1979-01-01

    The advantages of using psychometric thoery to design short forms of intelligence tests are demonstrated by comparing such usage to a systematic random procedure that has previously been used. The Wechsler Intelligence Scale for Children Revised (WISC-R) Short Form is presented as an example. (JKS)

  7. Test-Retest Reliability of the Short-Form Survivor Unmet Needs Survey.

    Science.gov (United States)

    Taylor, Karen; Bulsara, Max; Monterosso, Leanne

    2018-01-01

    Reliable and valid needs assessment measures are important assessment tools in cancer survivorship care. A new 30-item short-form version of the Survivor Unmet Needs Survey (SF-SUNS) was developed and validated with cancer survivors, including hematology cancer survivors; however, test-retest reliability has not been established. The objective of this study was to assess the test-retest reliability of the SF-SUNS with a cohort of lymphoma survivors ( n = 40). Test-retest reliability of the SF-SUNS was conducted at two time points: baseline (time 1) and 5 days later (time 2). Test-retest data were collected from lymphoma cancer survivors ( n = 40) in a large tertiary cancer center in Western Australia. Intraclass correlation analyses compared data at time 1 (baseline) and time 2 (5 days later). Cronbach's alpha analyses were performed to assess the internal consistency at both time points. The majority (23/30, 77%) of items achieved test-retest reliability scores 0.45-0.74 (fair to good). A high degree of overall internal consistency was demonstrated (time 1 = 0.92, time 2 = 0.95), with scores 0.65-0.94 across subscales for both time points. Mixed test-retest reliability of the SF-SUNS was established. Our results indicate the SF-SUNS is responsive to the changing needs of lymphoma cancer survivors. Routine use of cancer survivorship specific needs-based assessments is required in oncology care today. Nurses are well placed to administer these assessments and provide tailored information and resources. Further assessment of test-retest reliability in hematology and other cancer cohorts is warranted.

  8. Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.

    Science.gov (United States)

    Waddell, Peter J; Ota, Rissa; Penny, David

    2009-10-01

    Testing fit of data to model is fundamentally important to any science, but publications in the field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without cause, Popper (Unended quest: an intellectual autobiography. Fontana, London, 1976) once argued that evolutionary biology was unscientific as its hypotheses were untestable. Here we trace developments in assessing fit from Penny et al. (Nature 297:197-200, 1982) to the present. We compare the general log-likelihood ratio (the G or G (2) statistic) statistic between the evolutionary tree model and the multinomial model with that of marginalized tests applied to an alignment (using placental mammal coding sequence data). It is seen that the most general test does not reject the fit of data to model (P approximately 0.5), but the marginalized tests do. Tests on pairwise frequency (F) matrices, strongly (P < 0.001) reject the most general phylogenetic (GTR) models commonly in use. It is also clear (P < 0.01) that the sequences are not stationary in their nucleotide composition. Deviations from stationarity and homogeneity seem to be unevenly distributed amongst taxa; not necessarily those expected from examining other regions of the genome. By marginalizing the 4( t ) patterns of the i.i.d. model to observed and expected parsimony counts, that is, from constant sites, to singletons, to parsimony informative characters of a minimum possible length, then the likelihood ratio test regains power, and it too rejects the evolutionary model with P < 0.001. Given such behavior over relatively recent evolutionary time, readers in general should maintain a healthy skepticism of results, as the scale of the systematic errors in published trees may really be far larger than the analytical methods (e.g., bootstrap) report.

  9. In situ detection of a heat-shock regulatory element binding protein using a soluble short synthetic enhancer sequence

    Energy Technology Data Exchange (ETDEWEB)

    Harel-Bellan, A; Brini, A T; Farrar, W L [National Cancer Institute, Frederick, MD (USA); Ferris, D K [Program Resources, Inc., Frederick, MD (USA); Robin, P [Institut Gustave Roussy, Villejuif (France)

    1989-06-12

    In various studies, enhancer binding proteins have been successfully absorbed out by competing sequences inserted into plasmids, resulting in the inhibition of the plasmid expression. Theoretically, such a result could be achieved using synthetic enhancer sequences not inserted into plasmids. In this study, a double stranded DNA sequence corresponding to the human heat shock regulatory element was chemically synthesized. By in vitro retardation assays, the synthetic sequence was shown to bind specifically a protein in extracts from the human T cell line Jurkat. When the synthetic enhancer was electroporated into Jurkat cells, not only the enhancer was shown to remain undegraded into the cells for up to 2 days, but also its was shown to bind intracellularly a protein. The binding was specific and was modulated upon heat shock. Furthermore, the binding protein was shown to be of the expected molecular weight by UV crosslinking. However, when the synthetic enhancer element was co-electroporated with an HSP 70-CAT reporter construct, the expression of the reporter plasmid was consistently enhanced in the presence of the exogenous synthetic enhancer.

  10. Quantification of loading in biomechanical testing: the influence of dissection sequence.

    Science.gov (United States)

    Funabashi, Martha; El-Rich, Marwan; Prasad, Narasimha; Kawchuk, Gregory N

    2015-09-18

    Sequential dissection is a technique used to investigate loads experienced by articular tissues. When the joint of interest is tested in an unconstrained manner, its kinematics change with each tissue removal. To address this limitation, sufficiently rigid robots are used to constrain joint kinematics. While this approach can quantify loads experienced by each tissue, it does not assure similar results when removal order is changed. Specifically, structure loading is assumed to be independent of removal order if the structure behaves linearly (i.e. principle of superposition applies), but dependent on removal order when response is affected by material and/or geometry nonlinearities and/or viscoelasticiy (e.g. biological tissues). Therefore, this experiment was conducted to evaluate if structure loading created through robotic testing is dependent on the order in which connectors are removed. Six identical models were 3D printed. Each model was composed of 2 rigid bodies and 3 connecting structures with nonlinear time-dependent behavior. To these models, pure rotations were applied about a predefined static center of rotation using a parallel robot. A unique dissection sequence was used for each of the six models and the same movements applied robotically after each dissection. When comparing the moments experienced by each structure between different removal sequences, a statistically significant difference (probotic testing are specific to removal order. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. An exponential combination procedure for set-based association tests in sequencing studies.

    Science.gov (United States)

    Chen, Lin S; Hsu, Li; Gamazon, Eric R; Cox, Nancy J; Nicolae, Dan L

    2012-12-07

    State-of-the-art next-generation-sequencing technologies can facilitate in-depth explorations of the human genome by investigating both common and rare variants. For the identification of genetic factors that are associated with disease risk or other complex phenotypes, methods have been proposed for jointly analyzing variants in a set (e.g., all coding SNPs in a gene). Variants in a properly defined set could be associated with risk or phenotype in a concerted fashion, and by accumulating information from them, one can improve power to detect genetic risk factors. Many set-based methods in the literature are based on statistics that can be written as the summation of variant statistics. Here, we propose taking the summation of the exponential of variant statistics as the set summary for association testing. From both Bayesian and frequentist perspectives, we provide theoretical justification for taking the sum of the exponential of variant statistics because it is particularly powerful for sparse alternatives-that is, compared with the large number of variants being tested in a set, only relatively few variants are associated with disease risk-a distinctive feature of genetic data. We applied the exponential combination gene-based test to a sequencing study in anticancer pharmacogenomics and uncovered mechanistic insights into genes and pathways related to chemotherapeutic susceptibility for an important class of oncologic drugs. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  12. A functional test of Neandertal and modern human mitochondrial targeting sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gralle, Matthias, E-mail: gralle@bioqmed.ufrj.br [Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, CCS, Ilha do Fundao, 21941-590 Rio de Janeiro (Brazil); Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany); Schaefer, Ingo; Seibel, Peter [Department of Molecular Cell Therapy, Leipzig University, Deutscher Platz 5, 04103 Leipzig (Germany); Paeaebo, Svante [Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany)

    2010-11-26

    Research highlights: {yields} Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. {yields} The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. {yields} In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  13. A functional test of Neandertal and modern human mitochondrial targeting sequences

    International Nuclear Information System (INIS)

    Gralle, Matthias; Schaefer, Ingo; Seibel, Peter; Paeaebo, Svante

    2010-01-01

    Research highlights: → Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. → The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. → In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  14. Short-Run Contexts and Imperfect Testing for Continuous Sampling Plans

    Directory of Open Access Journals (Sweden)

    Mirella Rodriguez

    2018-04-01

    Full Text Available Continuous sampling plans are used to ensure a high level of quality for items produced in long-run contexts. The basic idea of these plans is to alternate between 100% inspection and a reduced rate of inspection frequency. Any inspected item that is found to be defective is replaced with a non-defective item. Because not all items are inspected, some defective items will escape to the customer. Analytical formulas have been developed that measure both the customer perceived quality and also the level of inspection effort. The analysis of continuous sampling plans does not apply to short-run contexts, where only a finite-size batch of items is to be produced. In this paper, a simulation algorithm is designed and implemented to analyze the customer perceived quality and the level of inspection effort for short-run contexts. A parameter representing the effectiveness of the test used during inspection is introduced to the analysis, and an analytical approximation is discussed. An application of the simulation algorithm that helped answer questions for the U.S. Navy is discussed.

  15. Short-term stability test for thorium soil candidate a reference material

    Energy Technology Data Exchange (ETDEWEB)

    Clain, Almir F.; Fonseca, Adelaide M.G.; Dantas, Vanessa V.D.B.; Braganca, Maura J.C.; Souza, Poliana S., E-mail: almir@ird.gov.br, E-mail: adelaide@ird.gov.br, E-mail: vanessa@ird.gov.br, E-mail: maura@ird.gov.br, E-mail: poliana@bolsista.ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2015-07-01

    This work describes a methodology to determine the soil short-term stability after the steps of production in laboratory. The short-term stability of the soil is an essential property to be determined in order to producing a reference material. The soil is a candidate of reference material for chemical analysis of thorium with metrological traceability to be used in environmental analysis, equipment calibration, validation methods, and quality control. A material is considered stable in a certain temperature if the property of interest does not change with time, considering the analytical random fluctuations. Due to this, the angular coefficient from the graphic of Th concentration versus elapsed time must be near to zero. The analytical determinations of thorium concentration were performed by Instrumental Neutron activation Analysis. The slopes and their uncertainties were obtained from the regression lines at temperatures of 20 deg C and 60 deg C, with control temperature of -20 deg C. From the obtained data a t-test was applied. In both temperatures the calculated t-value was lower than the critical value, so we can conclude with 95% confidence level that no significant changes happened during the period studied concerning thorium concentration in soil at temperatures of 20 deg C and 60 deg C, showing stability at these temperatures. (author)

  16. Short-circuit testing of monofilar Bi-2212 coils connected in series and in parallel

    International Nuclear Information System (INIS)

    Polasek, A; Dias, R; Serra, E T; Filho, O O; Niedu, D

    2010-01-01

    Superconducting Fault Current Limiters (SCFCL's) are one of the most promising technologies for fault current limitation. In the present work, resistive SCFCL components based on Bi-2212 monofilar coils are subjected to short-circuit testing. These SCFCL components can be easily connected in series and/or in parallel by using joints and clamps. This allows a considerable flexibility to developing larger SCFCL devices, since the configuration and size of the whole device can be easily adapted to the operational conditions. The single components presented critical current (Ic) values of 240-260 A, at 77 K. Short-circuits during 40-120 ms were applied. A single component can withstand a voltage drop of 126-252 V (0.3-0.6 V/cm). Components connected in series withstand higher voltage levels, whereas parallel connection allows higher rated currents during normal operation, but the limited current is also higher. Prospective currents as high as 10-40 kA (peak value) were limited to 3-9 kA (peak value) in the first half cycle.

  17. Short-term stability test for thorium soil candidate a reference material

    International Nuclear Information System (INIS)

    Clain, Almir F.; Fonseca, Adelaide M.G.; Dantas, Vanessa V.D.B.; Braganca, Maura J.C.; Souza, Poliana S.

    2015-01-01

    This work describes a methodology to determine the soil short-term stability after the steps of production in laboratory. The short-term stability of the soil is an essential property to be determined in order to producing a reference material. The soil is a candidate of reference material for chemical analysis of thorium with metrological traceability to be used in environmental analysis, equipment calibration, validation methods, and quality control. A material is considered stable in a certain temperature if the property of interest does not change with time, considering the analytical random fluctuations. Due to this, the angular coefficient from the graphic of Th concentration versus elapsed time must be near to zero. The analytical determinations of thorium concentration were performed by Instrumental Neutron activation Analysis. The slopes and their uncertainties were obtained from the regression lines at temperatures of 20 deg C and 60 deg C, with control temperature of -20 deg C. From the obtained data a t-test was applied. In both temperatures the calculated t-value was lower than the critical value, so we can conclude with 95% confidence level that no significant changes happened during the period studied concerning thorium concentration in soil at temperatures of 20 deg C and 60 deg C, showing stability at these temperatures. (author)

  18. A Methodological Approach for Testing the Viability of Seeds Stored in Short-Term Seed Banks

    Directory of Open Access Journals (Sweden)

    Jose A. FORTE GIL

    2017-12-01

    Full Text Available Efficient management of ‘active’ seed banks – specifically aimed at the short-term storage at room temperature of seeds to be used locally in conservation/regeneration programmes of endemic or endangered plant species – requires establishing the optimal storage time to maintain high seed viability, for each stored species. In this work, germination of seeds of the halophytes Thalictrum maritimum, Centaurea dracunculifolia and Linum maritimum has been investigated. The seeds had been stored for different periods of time in the seed bank of ‘La Albufera’ Natural Park (Valencia, SE Spain after collection in salt marshes of the Park, where small populations of the three species are present. Seeds of T. maritimum and C. dracunculifolia have a relatively short period of viability at room temperature, and should not be stored for more than three years. On the other hand, L. maritimum seeds maintain a high germination percentage and can be kept at room temperature for up to 10 years. T. maritimum seeds, in contrast to those of the other two species, did not germinate in in vitro tests nor when sown directly on a standard substrate, unless a pre-treatment of the seeds was applied, mechanical scarification being the most effective. These results will help to improve the management of the seed bank, to generate more efficiently new plants for reintroduction and reinforcement of populations of these species in their natural ecosystems within the Natural Park.

  19. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  20. Long- and short-term trends in vessel conditioning of TFTR [Tokamak Fusion Test Reactor

    International Nuclear Information System (INIS)

    LaMarche, P.H.; Dylla, H.F.; Bell, M.G.

    1986-10-01

    We have investigated trends in the conditioning of the Tokamak Fusion Test Reactor (TFTR) vacuum vessel during the May 1984 to April 1985 run period. The initial conditioning of the vessel, consisting of glow discharge cleaning (GDC) and pulse discharge cleaning (PDC) in concert with a 150 0 C vessel bakeout, is necessary to assure plasma operation after atmospheric venting. A long-term conditioning process, ascribed to limiter conditioning, effectively improves operational conditions during the course of the run. Over several thousand high power plasma discharges, the improvement was documented by using standard parameter (fiducial) plasma discharges. Several techniques demonstrated short-term improvements in vessel conditioning during this time period, including: Cr gettering and programming the plasma position relative to the limiter contact area

  1. Temporal stability of the Francis Scale of Attitude toward Christianity short-form: test-retest data over one week.

    Science.gov (United States)

    Lewis, Christopher Alan; Cruise, Sharon Mary; McGuckin, Conor

    2005-04-01

    This study evaluated the test-retest reliability of the Francis Scale of Attitude toward Christianity short-form. 39 Northern Irish undergraduate students completed the measure on two occasions separated by one week. Stability across the two administrations was high, r = .92, and there was no significant change between Time 1(M = 25.2, SD = 5.4) and Time 2 (M = 25.7, SD = 6.2). These data support the short-term test-retest reliability of the Francis Scale of Attitude toward Christianity short-form.

  2. "I know your name, but not your number"--Patients with verbal short-term memory deficits are impaired in learning sequences of digits.

    Science.gov (United States)

    Bormann, Tobias; Seyboth, Margret; Umarova, Roza; Weiller, Cornelius

    2015-06-01

    Studies on verbal learning in patients with impaired verbal short-term memory (vSTM) have revealed dissociations among types of verbal information. Patients with impaired vSTM are able to learn lists of known words but fail to acquire new word forms. This suggests that vSTM is involved in new word learning. The present study assessed both new word learning and the learning of digit sequences in two patients with impaired vSTM. In two experiments, participants were required to learn people's names, ages and professions, or their four digit 'phone numbers'. The STM patients were impaired on learning unknown family names and phone numbers, but managed to acquire other verbal information. In contrast, a patient with a severe verbal episodic memory impairment was impaired across information types. These results indicate verbal STM involvement in the learning of digit sequences. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. MRI in multiple sclerosis of the spinal cord: evaluation of fast short-tan inversion-recovery and spin-echo sequences

    International Nuclear Information System (INIS)

    Dietemann, J.L.; Thibaut-Menard, A.; Neugroschl, C.; Gillis, C.; Abu Eid, M.; Bogorin, A.; Warter, J.M.; Tranchant, C.

    2000-01-01

    We compared the sensitivity of T2-weighted spin-echo (FSE) and fast short-tau inversion-recovery (fSTIR) sequences in detection of multiple sclerosis of the spinal cord in 100 consecutive patients with clinically confirmed multiple sclerosis (MS); 86 patients underwent also brain MRI. In all, 310 focal lesions were detected on fSTIR and 212 on T2-weighted FSE, spinal cord lesions were seen better on fSTIR images, with a higher contrast between the lesion and the normal spinal cord. In 24 patients in whom cord plaques were shown with both sequences, the cranial study was normal or inconclusive. Assessment of spinal plaques can be particularly important when MRI of the brain is inconclusive, and in there situations fSTIR can be helpful. (orig.)

  4. Current research efforts at JILA to test the equivalence principle at short ranges

    International Nuclear Information System (INIS)

    Faller, J.E.; Niebauer, T.M.; McHugh, M.P.; Van Baak, D.A.

    1988-01-01

    We are presently engaged in three different experiments to search for a possible breakdown of the equivalence principle at short ranges. The first of these experiments, which has been completed, is our so-called Galilean test in which the differential free-fall of two objects of differing composition was measured using laser interferometry. We observed that the differential acceleration of two test bodies was less than 5 parts in 10 billion. This experiment set new limits on a suggested baryon dependent ''Fifth Force'' at ranges longer than 1 km. With a second experiment, we are investigating substance dependent interactions primarily for ranges up to 10 meters using a fluid supported torsion balance; this apparatus has been built and is now undergoing laboratory tests. Finally, a proposal has been made to measure the gravitational signal associated with the changing water level at a large pumped storage facility in Ludington, Michigan. Measuring the gravitational signal above and below the pond will yield the value of the gravitational constant, G, at ranges from 10-100 m. These measurements will serve as an independent check on other geophysical measurements of G

  5. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  6. Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

    Science.gov (United States)

    Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

    2011-07-01

    Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

  7. Characteristic interpersonal behavior in dependent and avoidant personality disorder can be observed within very short interaction sequences.

    Science.gov (United States)

    Leising, Daniel; Sporberg, Doreen; Rehbein, Diana

    2006-08-01

    We present a behavior observation study of interpersonal behavior in 96 female subjects, who had been screened for the presence of dependent, avoidant, narcissistic and histrionic personality disorder features. Each subject took part in three short role-plays, taken from assertiveness training. Afterwards, both the subject and her role-play partner judged, how assertive the subject had been. Although observation time was very short, dependent and avoidant subjects could be easily identified from their overly submissive behavior in the role-plays. Histrionic and narcissistic subjects did not show distinctive interpersonal behavior. Contrary to a common belief, higher scores on some personality disorder (PD) scales were positively related to cross-situational variability of behavior. Results are discussed with regard to their implications for clinical diagnostics, therapy and the methodology of personality disorder research in general.

  8. Multiple regulatory mechanisms of hepatocyte growth factor expression in malignant cells with a short poly(dA) sequence in the HGF gene promoter.

    Science.gov (United States)

    Sakai, Kazuko; Takeda, Masayuki; Okamoto, Isamu; Nakagawa, Kazuhiko; Nishio, Kazuto

    2015-01-01

    Hepatocyte growth factor (HGF) expression is a poor prognostic factor in various types of cancer. Expression levels of HGF have been reported to be regulated by shorter poly(dA) sequences in the promoter region. In the present study, the poly(dA) mononucleotide tract in various types of human cancer cell lines was examined and compared with the HGF expression levels in those cells. Short deoxyadenosine repeat sequences were detected in five of the 55 cell lines used in the present study. The H69, IM95, CCK-81, Sui73 and H28 cells exhibited a truncated poly(dA) sequence in which the number of poly(dA) repeats was reduced by ≥5 bp. Two of the cell lines exhibited high HGF expression, determined by reverse transcription quantitative polymerase chain reaction and enzyme-linked immunosorbent assay. The CCK-81, Sui73 and H28 cells with shorter poly(dA) sequences exhibited low HGF expression. The cause of the suppression of HGF expression in the CCK-81, Sui73 and H28 cells was clarified by two approaches, suppression by methylation and single nucleotide polymorphisms in the HGF gene. Exposure to 5-Aza-dC, an inhibitor of DNA methyltransferase 1, induced an increased expression of HGF in the CCK-81 cells, but not in the other cells. Single-nucleotide polymorphism (SNP) rs72525097 in intron 1 was detected in the Sui73 and H28 cells. Taken together, it was found that the defect of poly(dA) in the HGF promoter was present in various types of cancer, including lung, stomach, colorectal, pancreas and mesothelioma. The present study proposes the negative regulation mechanisms by methylation and SNP in intron 1 of HGF for HGF expression in cancer cells with short poly(dA).

  9. Are Soft Short Tests Good Indicators of Internal Li-ion Cell Defects?

    Science.gov (United States)

    Jeevarajan, J.; Chung, J.-S.; Jung, K.; Park, J.

    2013-01-01

    The self discharge test at full state of charge, may not be a good one to detect subtle defects since the li-ion chemistry has the highest self discharge at full state of charge. One should characterize self discharge versus storage time for each cell manufacturer/design to differentiate between normal self discharge and that due to a subtle manufacturing defect. The various soft short test methods indicate that if this test is carried out at full discharge (0% SOC) with all capacity removed (by lowering the current load in a stepwise manner to the same end of discharge voltage), then the cells need to be placed in storage for more than 72 hours to get a good analysis on the presence of subtle defects since it takes more than 72 hours to achieve voltage stabilization. If the cells are to be charged up even to a small percentage (ex. 1%), 72 hours are sufficient to determine issues. However, the pass/fail criteria should be based on a valid OCV decline. Less than 10 mV voltage decline is not a good method to detect subtle defects. As mentioned in the first bullet, self discharge is a competing reaction when a charge is introduced and hence a characterization of the self discharge versus storage time is required to fully correlate voltage decline to a failure due to a subtle defect. Soft short test method cannot be relied on for defect detection because cells with and without voltage decline seemed to have similar defects and characteristics. Screening methods such as internal resistance and capacity as well as a 3-sigma range for OCV, mass and dimensions should be used to screen out outliers. A very critical aspect in the understanding of subtle defects is to carry out destructive analysis of cells from every lot to confirm the quality of production and screen all cells and batteries in a stringent manner to have a high quality set of flight cells. Self Discharge Test: Fully charged cells shall be placed in Open circuit stand for 72 hours (OCV measurement twice a

  10. RECOGNIZING REFERENCES TO PHYSICAL PLACES INSIDE SHORT TEXTS BY USING PATTERNS AS A SEQUENCE OF GRAMMATICAL CATEGORIES

    Directory of Open Access Journals (Sweden)

    A. Romero

    2017-09-01

    Full Text Available Collecting data by crowdsourcing is an explored trend to support database population and update. This kind of data is unstructured and comes from text, in particular text in social networks. Geographic database is a particular case of database that can be populated by crowdsourcing which can be done when people report some urban event in a social network by writing a short message. An event can describe an accident or a non-functioning device in the urban area. The authorities then need to read and to interpret the message to provide some help for injured people or to fix a problem in a device installed in the urban area like a light or a problem on road. Our main interest is located on working with short messages organized in a collection. Most of the messages do not have geographical coordinates. The messages can then be classified by text patterns describing a location. In fact, people use a text pattern to describe an urban location. Our work tries to identify patterns inside a short text and to indicate when it describes a location. When a pattern is identified our approach look to describe the place where the event is located. The source messages used are tweets reporting events from several Mexican cities.

  11. Recognizing References to Physical Places Inside Short Texts by Using Patterns as a Sequence of Grammatical Categories

    Science.gov (United States)

    Romero, A.; Sol, D.

    2017-09-01

    Collecting data by crowdsourcing is an explored trend to support database population and update. This kind of data is unstructured and comes from text, in particular text in social networks. Geographic database is a particular case of database that can be populated by crowdsourcing which can be done when people report some urban event in a social network by writing a short message. An event can describe an accident or a non-functioning device in the urban area. The authorities then need to read and to interpret the message to provide some help for injured people or to fix a problem in a device installed in the urban area like a light or a problem on road. Our main interest is located on working with short messages organized in a collection. Most of the messages do not have geographical coordinates. The messages can then be classified by text patterns describing a location. In fact, people use a text pattern to describe an urban location. Our work tries to identify patterns inside a short text and to indicate when it describes a location. When a pattern is identified our approach look to describe the place where the event is located. The source messages used are tweets reporting events from several Mexican cities.

  12. Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease.

    Science.gov (United States)

    Ellingford, Jamie M; Barton, Stephanie; Bhaskar, Sanjeev; Williams, Simon G; Sergouniotis, Panagiotis I; O'Sullivan, James; Lamb, Janine A; Perveen, Rahat; Hall, Georgina; Newman, William G; Bishop, Paul N; Roberts, Stephen A; Leach, Rick; Tearle, Rick; Bayliss, Stuart; Ramsden, Simon C; Nemeth, Andrea H; Black, Graeme C M

    2016-05-01

    To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Case series. A total of 562 patients diagnosed with IRD. We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Diagnostic yield of genomic testing. Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield. We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  13. Morpho-Functional 1H-MRI of the Lung in COPD: Short-Term Test-Retest Reliability.

    Directory of Open Access Journals (Sweden)

    Bertram J Jobst

    Full Text Available Non-invasive end-points for interventional trials and tailored treatment regimes in chronic obstructive pulmonary disease (COPD for monitoring regionally different manifestations of lung disease instead of global assessment of lung function with spirometry would be valuable. Proton nuclear magnetic resonance imaging (1H-MRI allows for a radiation-free assessment of regional structure and function. The aim of this study was to evaluate the short-term reproducibility of a comprehensive morpho-functional lung MRI protocol in COPD.20 prospectively enrolled COPD patients (GOLD I-IV underwent 1H-MRI of the lung at 1.5T on two consecutive days, including sequences for morphology, 4D contrast-enhanced perfusion, and respiratory mechanics. Image quality and COPD-related morphological and functional changes were evaluated in consensus by three chest radiologists using a dedicated MRI-based visual scoring system. Test-retest reliability was calculated per each individual lung lobe for the extent of large airway (bronchiectasis, wall thickening, mucus plugging and small airway abnormalities (tree in bud, peripheral bronchiectasis, mucus plugging, consolidations, nodules, parenchymal defects and perfusion defects. The presence of tracheal narrowing, dystelectasis, pleural effusion, pulmonary trunk ectasia, right ventricular enlargement and, finally, motion patterns of diaphragma and chest wall were addressed.Median global scores [10(Q1:8.00;Q3:16.00 vs.11(Q1:6.00;Q3:15.00] as well as category subscores were similar between both timepoints, and kappa statistics indicated "almost perfect" global agreement (ĸ = 0.86, 95%CI = 0.81-0.91. Most subscores showed at least "substantial" agreement of MRI1 and MRI2 (ĸ = 0.64-1.00, whereas the agreement for the diagnosis of dystelectasis/effusion (ĸ = 0.42, 95%CI = 0.00-0.93 was "moderate" and of tracheal abnormalities (ĸ = 0.21, 95%CI = 0.00-0.75 "fair". Most MRI acquisitions showed at least diagnostic quality at

  14. Effects of an Inquiry-Based Short Intervention on State Test Anxiety in Comparison to Alternative Coping Strategies

    Directory of Open Access Journals (Sweden)

    Ann Krispenz

    2018-02-01

    Full Text Available Background and Objectives: Test anxiety can have undesirable consequences for learning and academic achievement. The control-value theory of achievement emotions assumes that test anxiety is experienced if a student appraises an achievement situation as important (value appraisal, but feels that the situation and its outcome are not fully under his or her control (control appraisal. Accordingly, modification of cognitive appraisals is assumed to reduce test anxiety. One method aiming at the modification of appraisals is inquiry-based stress reduction. In the present study (N = 162, we assessed the effects of an inquiry-based short intervention on test anxiety.Design: Short-term longitudinal, randomized control trial.Methods: Focusing on an individual worry thought, 53 university students received an inquiry-based short intervention. Control participants reflected on their worry thought (n = 55 or were distracted (n = 52. Thought related test anxiety was assessed before, immediately after, and 2 days after the experimental treatment.Results: After the intervention as well as 2 days later, individuals who had received the inquiry-based intervention demonstrated significantly lower test anxiety than participants from the pooled control groups. Further analyses showed that the inquiry-based short intervention was more effective than reflecting on a worry thought but had no advantage over distraction.Conclusions: Our findings provide first experimental evidence for the effectiveness of an inquiry-based short intervention in reducing students’ test anxiety.

  15. Towards automatic recognition of irregular, short-open answers in Fill-in-the-blank tests

    Directory of Open Access Journals (Sweden)

    Sergio A. Rojas

    2014-01-01

    Full Text Available Assessment of student knowledge in Learning Management Systems such as Moodle is mostly conducted using close-ended questions (e.g. multiple-choice whose answers are straightforward to grade without human intervention. FILL-IN-THE-BLANK tests are usually more challenging since they require test-takers to recall concepts and associations not available in the statement of the question itself (no choices or hints are given. Automatic assessment of the latter currently requires the test-taker to give a verbatim answer, that is, free of spelling or typographical mistakes. In this paper, we consider an adapted version of a classical text-matching algorithm that may prevent wrong grading in automatic assessment of FILL-IN-THE-BLANK questions whenever irregular (similar but not exact answers occur due to such types of error. The technique was tested in two scenarios. In the first scenario, misspelled single-word answers to an Internet security questionnaire were correctly recognized within a two letter editing tolerance (achieving 99 % accuracy. The second scenario involved short-open answers to computer programming quizzes (i.e. small blocks of code requiring a structure that conforms to the syntactic rules of the programming language. Twenty-one real-world answers written up by students, taking a computer programming course, were assessed by the method. This assessment addressed the lack of precision in terms of programmer-style artifacts (such as unfamiliar variable or function nomenclature and uses an admissible tolerance of up to 20 % letter-level typos. These scores were satisfactory corroborated by a human expert. Additional findings and potential enhancements to the technique are also discussed.

  16. Testing gravitational parity violation with coincident gravitational waves and short gamma-ray bursts

    International Nuclear Information System (INIS)

    Yunes, Nicolas; O'Shaughnessy, Richard; Owen, Benjamin J.; Alexander, Stephon

    2010-01-01

    Gravitational parity violation is a possibility motivated by particle physics, string theory, and loop quantum gravity. One effect of it is amplitude birefringence of gravitational waves, whereby left and right circularly polarized waves propagate at the same speed but with different amplitude evolution. Here we propose a test of this effect through coincident observations of gravitational waves and short gamma-ray bursts from binary mergers involving neutron stars. Such gravitational waves are highly left or right circularly polarized due to the geometry of the merger. Using localization information from the gamma-ray burst, ground-based gravitational wave detectors can measure the distance to the source with reasonable accuracy. An electromagnetic determination of the redshift from an afterglow or host galaxy yields an independent measure of this distance. Gravitational parity violation would manifest itself as a discrepancy between these two distance measurements. We exemplify such a test by considering one specific effective theory that leads to such gravitational parity violation, Chern-Simons gravity. We show that the advanced LIGO-Virgo network and all-sky gamma-ray telescopes can be sensitive to the propagating sector of Chern-Simons gravitational parity violation to a level roughly 2 orders of magnitude better than current stationary constraints from the LAGEOS satellites.

  17. LISA Pathfinder test-mass charging during galactic cosmic-ray flux short-term variations

    Science.gov (United States)

    Grimani, C.; Fabi, M.; Lobo, A.; Mateos, I.; Telloni, D.

    2015-02-01

    Metal free-floating test masses aboard the future interferometers devoted to gravitational wave detection in space are charged by galactic and solar cosmic rays with energies \\gt 100 MeV/n. This process represents one of the main sources of noise in the lowest frequency band (\\lt 10-3 Hz) of these experiments. We study here the charging of the LISA Pathfinder (LISA-PF) gold-platinum test masses due to galactic cosmic-ray (GCR) protons and helium nuclei with the Fluka Monte Carlo toolkit. Projections of the energy spectra of GCRs during the LISA-PF operations in 2015 are considered. This work was carried out on the basis of the solar activity level and solar polarity epoch expected for LISA-PF. The effects of GCR short-term variations are evaluated here for the first time. Classical Forbush decreases, GCR variations induced by the Sun rotation, and fluctuations in the LISA-PF frequency bandwidth are discussed.

  18. A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology.

    Science.gov (United States)

    Vissers, Lisenka E L M; van Nimwegen, Kirsten J M; Schieving, Jolanda H; Kamsteeg, Erik-Jan; Kleefstra, Tjitske; Yntema, Helger G; Pfundt, Rolph; van der Wilt, Gert Jan; Krabbenborg, Lotte; Brunner, Han G; van der Burg, Simone; Grutters, Janneke; Veltman, Joris A; Willemsen, Michèl A A P

    2017-09-01

    Implementation of novel genetic diagnostic tests is generally driven by technological advances because they promise shorter turnaround times and/or higher diagnostic yields. Other aspects, including impact on clinical management or cost-effectiveness, are often not assessed in detail prior to implementation. We studied the clinical utility of whole-exome sequencing (WES) in complex pediatric neurology in terms of diagnostic yield and costs. We analyzed 150 patients (and their parents) presenting with complex neurological disorders of suspected genetic origin. In a parallel study, all patients received both the standard diagnostic workup (e.g., cerebral imaging, muscle biopsies or lumbar punctures, and sequential gene-by-gene-based testing) and WES simultaneously. Our unique study design allowed direct comparison of diagnostic yield of both trajectories and provided insight into the economic implications of implementing WES in this diagnostic trajectory. We showed that WES identified significantly more conclusive diagnoses (29.3%) than the standard care pathway (7.3%) without incurring higher costs. Exploratory analysis of WES as a first-tier diagnostic test indicates that WES may even be cost-saving, depending on the extent of other tests being omitted. Our data support such a use of WES in pediatric neurology for disorders of presumed genetic origin.Genet Med advance online publication 23 March 2017.

  19. Alternative short tests for inspection and maintenance of in-use cars with respect to their emissions performance

    NARCIS (Netherlands)

    Samaras, Z.; Zachariadis, T.; Joumard, R.; Vernet, I.; Hassel, D.; Weber, F.-J.; Rijkeboer, R.C.

    1998-01-01

    This paper presents the first results of a project aimed at evaluation of a number of short tests that can be alternatively used for Inspection and Maintenance of in-use cars emissions performance. For this purpose, a large number of in-use cars from four European countries was tested according to a

  20. A comparison of discriminant logistic regression and Item Response Theory Likelihood-Ratio Tests for Differential Item Functioning (IRTLRDIF) in polytomous short tests.

    Science.gov (United States)

    Hidalgo, María D; López-Martínez, María D; Gómez-Benito, Juana; Guilera, Georgina

    2016-01-01

    Short scales are typically used in the social, behavioural and health sciences. This is relevant since test length can influence whether items showing DIF are correctly flagged. This paper compares the relative effectiveness of discriminant logistic regression (DLR) and IRTLRDIF for detecting DIF in polytomous short tests. A simulation study was designed. Test length, sample size, DIF amount and item response categories number were manipulated. Type I error and power were evaluated. IRTLRDIF and DLR yielded Type I error rates close to nominal level in no-DIF conditions. Under DIF conditions, Type I error rates were affected by test length DIF amount, degree of test contamination, sample size and number of item response categories. DLR showed a higher Type I error rate than did IRTLRDIF. Power rates were affected by DIF amount and sample size, but not by test length. DLR achieved higher power rates than did IRTLRDIF in very short tests, although the high Type I error rate involved means that this result cannot be taken into account. Test length had an important impact on the Type I error rate. IRTLRDIF and DLR showed a low power rate in short tests and with small sample sizes.

  1. Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

    Science.gov (United States)

    Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J Antonio; Castro-Escarpulli, Graciela

    2015-08-04

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes. The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in

  2. Development of a short sample test facility for evaluating superconducting wires

    International Nuclear Information System (INIS)

    Singh, M.R.; Kulkarni, D.G.; Sahni, V.C.; Ravikumar, G.; Patel, K.L.

    2002-01-01

    In this paper we describe a short sample test facility we have set up at Bhabha Atomic Research Centre (BARC). This facility has been used to measure critical currents of NbTi/Cu composite superconducting wires by recording V versus I data at 4.2 K. It offers sample current as large as 1500 A and a transverse magnetic field up to 7.4 T. A power law, V ∼I n( H) is fitted to the resistive transition region to estimate the exponent n, which is a measure of the uniformity of superconducting filaments in composite wires. It is observed that inadequate thermal stabilization of sample wire results in thermal runaway, which limits the V-I data to∼ 2μ V . This in turn affects the reliability of estimated filament uniformity. To mitigate this problem, we have used a sample holder made of OFHC-Cu which enhances thermal stabilization of the sample. With this sample holder, the results of measurements carried out on wires developed by the Atomic Fuel Division, BARC show a high filament uniformity (n ∼ 58). (author)

  3. Performance Tests of a Short Faraday Cup Designed for HIE-ISOLDE

    CERN Document Server

    Cantero, E; Bravin, E; Fraser, M; Lanaia, D; Sosa, A; Voulot, D

    2013-01-01

    The On-Line Isotope Mass Separator (ISOLDE) facility at CERN is being upgraded in order to deliver higher energy and intensity radioactive beams. The final setup will consist in replacing the energy variable part of the normal conducting REX post-accelerator with superconducting cavities. In order to preserve the beam emittance, the drift space between the cryomodules housing these cavities has been kept to a minimum. As a consequence, the longitudinal space available for beam diagnostics is severely limited in the inter-cryomodule regions. A Faraday cup (FC) will be installed to measure beam currents, and due to the tight spatial constraints, its length is much smaller than usual. This poses a great challenge when trying to avoid the escape of ion-induced secondary electrons, which would falsify the current measurement. Two prototypes of such a short FC have therefore been tested at REX-ISOLDE using several beam intensities and energies, with the aim of determining its accuracy. In this paper the experimenta...

  4. Ultra-high accuracy optical testing: creating diffraction-limited short-wavelength optical systems

    International Nuclear Information System (INIS)

    Goldberg, Kenneth A.; Naulleau, Patrick P.; Rekawa, Senajith B.; Denham, Paul E.; Liddle, J. Alexander; Gullikson, Eric M.; Jackson, KeithH.; Anderson, Erik H.; Taylor, John S.; Sommargren, Gary E.; Chapman, Henry N.; Phillion, Donald W.; Johnson, Michael; Barty, Anton; Soufli, Regina; Spiller, Eberhard A.; Walton, Christopher C.; Bajt, Sasa

    2005-01-01

    Since 1993, research in the fabrication of extreme ultraviolet (EUV) optical imaging systems, conducted at Lawrence Berkeley National Laboratory (LBNL) and Lawrence Livermore National Laboratory (LLNL), has produced the highest resolution optical systems ever made. We have pioneered the development of ultra-high-accuracy optical testing and alignment methods, working at extreme ultraviolet wavelengths, and pushing wavefront-measuring interferometry into the 2-20-nm wavelength range (60-600 eV). These coherent measurement techniques, including lateral shearing interferometry and phase-shifting point-diffraction interferometry (PS/PDI) have achieved RMS wavefront measurement accuracies of 0.5-1-(angstrom) and better for primary aberration terms, enabling the creation of diffraction-limited EUV optics. The measurement accuracy is established using careful null-testing procedures, and has been verified repeatedly through high-resolution imaging. We believe these methods are broadly applicable to the advancement of short-wavelength optical systems including space telescopes, microscope objectives, projection lenses, synchrotron beamline optics, diffractive and holographic optics, and more. Measurements have been performed on a tunable undulator beamline at LBNL's Advanced Light Source (ALS), optimized for high coherent flux; although many of these techniques should be adaptable to alternative ultraviolet, EUV, and soft x-ray light sources. To date, we have measured nine prototype all-reflective EUV optical systems with NA values between 0.08 and 0.30 (f/6.25 to f/1.67). These projection-imaging lenses were created for the semiconductor industry's advanced research in EUV photolithography, a technology slated for introduction in 2009-13. This paper reviews the methods used and our program's accomplishments to date

  5. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  6. Characterization of new eye drops with choline salicylate and assessment of their irritancy by in vitro short time exposure tests.

    Science.gov (United States)

    Wroblewska, Katarzyna; Kucinska, Małgorzata; Murias, Marek; Lulek, Janina

    2015-09-01

    The aim of our study was to examine the irritation potential of new eye drops containing 2% choline salicylate (CS) as an active pharmaceutical ingredient (API) and various polymers increasing eye drop viscosity (hydroxyethylcellulose, hydroxypropyl methylcellulose, methylcellulose, polyvinyl alcohol, polyvinylpyrrolidone). The standard method for assessing the potential of irritating substances has been the Draize rabbit eye test. However the European Centre for Validation of Alternative Methods and the Coordinating Committee for Validation of Alternative Methods recommend, short time exposure (STE) in vitro tests as an alternative method for assessing eye irritation. The eye irritation potential was determined using cytotoxicity test methods for rabbit corneal cell line (SIRC) after 5 min exposure. The viability of cells was determined using two cytotoxicity assays: MTT and Neutral Red Uptake. According to the irritation rankings for the short time exposure test, all tested eye drops are classified as non-irritating (cell viability >70%).

  7. Computational Bench Testing to Evaluate the Short-Term Mechanical Performance of a Polymeric Stent.

    Science.gov (United States)

    Bobel, A C; Petisco, S; Sarasua, J R; Wang, W; McHugh, P E

    2015-12-01

    Over the last decade, there has been a significant volume of research focussed on the utilization of biodegradable polymers such as poly-L-lactide-acid (PLLA) for applications associated with cardiovascular disease. More specifically, there has been an emphasis on upgrading current clinical shortfalls experienced with conventional bare metal stents and drug eluting stents. One such approach, the adaption of fully formed polymeric stents has led to a small number of products being commercialized. Unfortunately, these products are still in their market infancy, meaning there is a clear non-occurrence of long term data which can support their mechanical performance in vivo. Moreover, the load carry capacity and other mechanical properties essential to a fully optimized polymeric stent are difficult, timely and costly to establish. With the aim of compiling rapid and representative performance data for specific stent geometries, materials and designs, in addition to reducing experimental timeframes, Computational bench testing via finite element analysis (FEA) offers itself as a very powerful tool. On this basis, the research presented in this paper is concentrated on the finite element simulation of the mechanical performance of PLLA, which is a fully biodegradable polymer, in the stent application, using a non-linear viscous material model. Three physical stent geometries, typically used for fully polymeric stents, are selected, and a comparative study is performed in relation to their short-term mechanical performance, with the aid of experimental data. From the simulated output results, an informed understanding can be established in relation to radial strength, flexibility and longitudinal resistance, that can be compared with conventional permanent metal stent functionality, and the results show that it is indeed possible to generate a PLLA stent with comparable and sufficient mechanical performance. The paper also demonstrates the attractiveness of FEA as a tool

  8. LKM-1 autoantibodies recognize a short linear sequence in P450IID6, a cytochrome P-450 monooxygenase.

    OpenAIRE

    Manns, M P; Griffin, K J; Sullivan, K F; Johnson, E F

    1991-01-01

    LKM-1 autoantibodies, which are associated with autoimmune chronic active hepatitis, recognize P450IID6, a cytochrome P-450 monooxygenase. The reactivities of 26 LKM-1 antisera were tested with a panel of deletion mutants of P450IID6 expressed in Escherichia coli. 22 sera recognize a 33-amino acid segment of P450IID6, and 11 of these recognize a shorter segment, DPAQPPRD. PAQPPR is also found in IE175 of herpes simplex virus type 1 (HSV-1). Antibodies for HSV-1 proteins were detected by ELISA...

  9. A Test Bed for Short Pulse OA Detection of Optical Directors in Amphibious Operations

    National Research Council Canada - National Science Library

    Ertem, M

    1999-01-01

    ...) system to detect optical directors of potential threats in amphibious operations. The use of a short pulse duration allows discrimination of retroreflections from natural sources such as rock formations and vegetation...

  10. Retrieval practice with short-answer, multiple-choice, and hybrid tests.

    Science.gov (United States)

    Smith, Megan A; Karpicke, Jeffrey D

    2014-01-01

    Retrieval practice improves meaningful learning, and the most frequent way of implementing retrieval practice in classrooms is to have students answer questions. In four experiments (N=372) we investigated the effects of different question formats on learning. Students read educational texts and practised retrieval by answering short-answer, multiple-choice, or hybrid questions. In hybrid conditions students first attempted to recall answers in short-answer format, then identified answers in multiple-choice format. We measured learning 1 week later using a final assessment with two types of questions: those that could be answered by recalling information verbatim from the texts and those that required inferences. Practising retrieval in all format conditions enhanced retention, relative to a study-only control condition, on both verbatim and inference questions. However, there were little or no advantages of answering short-answer or hybrid format questions over multiple-choice questions in three experiments. In Experiment 4, when retrieval success was improved under initial short-answer conditions, there was an advantage of answering short-answer or hybrid questions over multiple-choice questions. The results challenge the simple conclusion that short-answer questions always produce the best learning, due to increased retrieval effort or difficulty, and demonstrate the importance of retrieval success for retrieval-based learning activities.

  11. Evaluation of the E mu-pim-1 transgenic mouse model for short-term carcinogenicity testing

    DEFF Research Database (Denmark)

    van Kreijl, C. F.; van Oordt, C. W. V.; Kroese, E. D.

    1998-01-01

    of T-cell lymphomas. Because of the low incidence of spontaneous tumors and the increased sensitivity to N-ethyl-N-nitrosourea-induced carcinogenesis, E mu-pim-1 mice were suggested to be one of the first potential and attractive candidates to be used in short-term carcinogenicity testing...

  12. Using the Δ3 statistic to test for missed levels in mixed sequence neutron resonance data

    International Nuclear Information System (INIS)

    Mulhall, Declan

    2009-01-01

    The Δ 3 (L) statistic is studied as a tool to detect missing levels in the neutron resonance data where two sequences are present. These systems are problematic because there is no level repulsion, and the resonances can be too close to resolve. Δ 3 (L) is a measure of the fluctuations in the number of levels in an interval of length L on the energy axis. The method used is tested on ensembles of mixed Gaussian orthogonal ensemble spectra, with a known fraction of levels (x%) randomly depleted, and can accurately return x. The accuracy of the method as a function of spectrum size is established. The method is used on neutron resonance data for 11 isotopes with either s-wave neutrons on odd-A isotopes, or p-wave neutrons on even-A isotopes. The method compares favorably with a maximum likelihood method applied to the level spacing distribution. Nuclear data ensembles were made from 20 isotopes in total, and their Δ 3 (L) statistics are discussed in the context of random matrix theory.

  13. Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data.

    Science.gov (United States)

    Mi, Gu; Di, Yanming; Schafer, Daniel W

    2015-01-01

    This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing (RNA-Seq) data analysis. The typically small number of biological samples and large number of genes in RNA-Seq analysis motivate us to address the trade-offs between robustness and statistical power using NB regression models. One widely-used power-saving strategy, for example, is to assume some commonalities of NB dispersion parameters across genes via simple models relating them to mean expression rates, and many such models have been proposed. As RNA-Seq analysis is becoming ever more popular, it is appropriate to make more thorough investigations into power and robustness of the resulting methods, and into practical tools for model assessment. In this article, we propose simulation-based statistical tests and diagnostic graphics to address model adequacy. We provide simulated and real data examples to illustrate that our proposed methods are effective for detecting the misspecification of the NB mean-variance relationship as well as judging the adequacy of fit of several NB dispersion models.

  14. Motor competence assessment in children: convergent and discriminant validity between the BOT-2 Short Form and KTK testing batteries.

    Science.gov (United States)

    Fransen, Job; D'Hondt, Eva; Bourgois, Jan; Vaeyens, Roel; Philippaerts, Renaat M; Lenoir, Matthieu

    2014-06-01

    This study investigated convergent and discriminant validity between two motor competence assessment instruments in 2485 Flemish children: the Bruininks-Oseretsky Test of Motor Proficiency 2 Short Form (BOT-2 Short Form) and the KörperKoördinationsTest für Kinder (KTK). A Pearson correlation assessed the relationship between BOT-2 Short Form total, gross and fine motor composite scores and KTK Motor Quotient in three age cohorts (6-7, 8-9, 10-11 years). Crosstabs were used to measure agreement in classification in children scoring below percentile 5 and 15 and above percentile 85 and 95. Moderately strong positive (r=0.44-0.64) associations between BOT-2 total and gross motor composite scores and KTK Motor Quotient and weak positive correlations between BOT-2 Short Form fine motor composite and KTK Motor Quotient scores (r=0.25-0.37) were found. Levels of agreement were fair to moderate. Therefore, some proof of convergent and discriminant validity between BOT-2 Short Form and KTK was established in this study, underlining the notion that the evaluation of motor competence should not be based upon a single assessment instrument. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

    Science.gov (United States)

    Jonker, Tanya R.; MacLeod, Colin M.

    2017-01-01

    Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

  16. Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

    Science.gov (United States)

    Barionovi, D; Giorgi, S; Stoeger, A R; Ruppitsch, W; Scortichini, M

    2006-05-01

    The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic

  17. Single-variant and multi-variant trend tests for genetic association with next-generation sequencing that are robust to sequencing error.

    Science.gov (United States)

    Kim, Wonkuk; Londono, Douglas; Zhou, Lisheng; Xing, Jinchuan; Nato, Alejandro Q; Musolf, Anthony; Matise, Tara C; Finch, Stephen J; Gordon, Derek

    2012-01-01

    As with any new technology, next-generation sequencing (NGS) has potential advantages and potential challenges. One advantage is the identification of multiple causal variants for disease that might otherwise be missed by SNP-chip technology. One potential challenge is misclassification error (as with any emerging technology) and the issue of power loss due to multiple testing. Here, we develop an extension of the linear trend test for association that incorporates differential misclassification error and may be applied to any number of SNPs. We call the statistic the linear trend test allowing for error, applied to NGS, or LTTae,NGS. This statistic allows for differential misclassification. The observed data are phenotypes for unrelated cases and controls, coverage, and the number of putative causal variants for every individual at all SNPs. We simulate data considering multiple factors (disease mode of inheritance, genotype relative risk, causal variant frequency, sequence error rate in cases, sequence error rate in controls, number of loci, and others) and evaluate type I error rate and power for each vector of factor settings. We compare our results with two recently published NGS statistics. Also, we create a fictitious disease model based on downloaded 1000 Genomes data for 5 SNPs and 388 individuals, and apply our statistic to those data. We find that the LTTae,NGS maintains the correct type I error rate in all simulations (differential and non-differential error), while the other statistics show large inflation in type I error for lower coverage. Power for all three methods is approximately the same for all three statistics in the presence of non-differential error. Application of our statistic to the 1000 Genomes data suggests that, for the data downloaded, there is a 1.5% sequence misclassification rate over all SNPs. Finally, application of the multi-variant form of LTTae,NGS shows high power for a number of simulation settings, although it can have

  18. Psychometric evaluation of the Chinese version of short-form Test of Functional Health Literacy in Adolescents.

    Science.gov (United States)

    Chang, Li-Chun; Hsieh, Pei-Lin; Liu, Chieh-Hsing

    2012-09-01

    The purpose of this study is to develop and evaluate the psychometric properties of the Chinese version of short-form Test of Functional Health Literacy in Adolescents. Assessing health literacy is vital to design health education programme; however, there are no measurement tools exist for use specifically in Chinese adolescents. A non-experimental design was used to test the psychometric properties of the Test of Functional Health Literacy in Adolescents. The short-form Test of Functional Health Literacy in Adolescents was translated and back translated into a Chinese language version. Thirty high school students were recruited to validate the scenario of Test of Functional Health Literacy in Adolescents. Based on the multiple-stage stratified random sampling method, 300 high school students from four counties in Taiwan were invited to participate in this study to evaluate the psychometric properties of Test of Functional Health Literacy in Adolescents. The Functional Health Literacy in Adolescents had good internal consistency reliability and excellent test-retest reliability. Confirmatory factor analysis resulted in a one-factor solution. Contrary to the original version of the Test of Functional Health Literacy in Adolescents, the findings revealed that the 36-item, one-factor model for the Test of Functional Health Literacy in Adolescents is the best-fit model. This is a suitable instrument to assess health literacy levels in Chinese adolescents before health education programmes can be appropriately planned, implemented and evaluated. © 2012 Blackwell Publishing Ltd.

  19. Selecting short-statured children needing growth hormone testing: Derivation and validation of a clinical decision rule

    Directory of Open Access Journals (Sweden)

    Bréart Gérard

    2008-07-01

    Full Text Available Abstract Background Numerous short-statured children are evaluated for growth hormone (GH deficiency (GHD. In most patients, GH provocative tests are normal and are thus in retrospect unnecessary. Methods A retrospective cohort study was conducted to identify predictors of growth hormone (GH deficiency (GHD in children seen for short stature, and to construct a very sensitive and fairly specific predictive tool to avoid unnecessary GH provocative tests. GHD was defined by the presence of 2 GH concentration peaks Results The initial study included 167 patients, 36 (22% of whom had GHD, including 5 (3% with certain GHD. Independent predictors of GHD were: growth rate Conclusion We have derived and performed an internal validation of a highly sensitive decision rule that could safely help to avoid more than 2/3 of the unnecessary GH tests. External validation of this rule is needed before any application.

  20. A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

    Directory of Open Access Journals (Sweden)

    Bárbara Angulo

    Full Text Available The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry, with direct sequencing and to investigate the limit of detection (LOD of both PCR-based methods. We identified EGFR mutations in 21 (16% of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%, which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%. Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+ yielded similar results. Immunohistochemistry (IHC staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

  1. Comparison of Short-Term Estrogenicity Tests for Identification of Hormone-Disrupting Chemicals

    DEFF Research Database (Denmark)

    Andersen, Helle Raun; Andersson, Anna-Maria; Arnold, Steven F.

    1999-01-01

    The aim of this study was to compare results obtained by eight different short-term assays of estrogenlike actions of chemicals conducted in 10 different laboratories in five countries. Twenty chemicals were selected to represent direct-acting estrogens, compounds with estrogenic metabolites, est...

  2. Comparison of short-term estrogenicity tests for identification of hormone-disrupting chemicals

    DEFF Research Database (Denmark)

    Andersen, H R; Andersson, A M; Arnold, S F

    1999-01-01

    The aim of this study was to compare results obtained by eight different short-term assays of estrogenlike actions of chemicals conducted in 10 different laboratories in five countries. Twenty chemicals were selected to represent direct-acting estrogens, compounds with estrogenic metabolites, est...

  3. A Single Lab Test to Aid Pierre Robin Sequence Severity Diagnosis.

    Science.gov (United States)

    Fahradyan, Artur; Azadgoli, Beina; Tsuha, Michaela; Urata, Mark M; Francis, Stacey H

    2018-01-01

    The workup of patients with Pierre Robin sequence (PRS) consists of a physical examination, O 2 saturation, and polysomnography to determine the severity of respiratory obstruction and need for surgery. We suggest that capillary blood gas (CBG) may be a better physiologic representation of airway obstruction and should be routinely used in the management of patients with PRS. This is a multicenter study based on a retrospective review of medical records. The study was performed at tertiary care centers. Patients with PRS <1 year old underwent mandibular distraction osteogenesis. Using successful treatment outcome as a reference standard, receiver operating characteristic (ROC) curve was used to determine the accuracy of the diagnostic test and values for the best sensitivity and specificity to determine the need for surgical intervention. Of 73 patients, 48 had sporadic PRS, 23 had syndromes, 2 had micrognathia, not otherwise specified. Mandibular distraction osteogenesis was performed in 62 patients at a mean age of 39 days. The mean initial Apnea-Hypopnea Index (AHI) in nonsurgical versus surgical groups was 10 versus 31 ( P = .063), pH 7.41 versus 7.34 ( P = .003), pCO 2 43 versus 56 ( P < .001), and HCO 3 27 versus 30 ( P = .022). The ROC curve showed that pCO 2 of 49.5 has the best specificity (100%) and sensitivity (72.6%) profile in terms of need for definitive airway. A simple CBG heel stick may better predict the physiologic effects of obstructive apnea; therefore, it should be added to the algorithm of PRS workup.

  4. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing.

    Science.gov (United States)

    Chimukangara, Benjamin; Varyani, Bhavini; Shamu, Tinei; Mutsvangwa, Junior; Manasa, Justen; White, Elizabeth; Chimbetete, Cleophas; Luethy, Ruedi; Katzenstein, David

    2017-05-01

    HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Concurrent Validity and Feasibility of Short Tests Currently Used to Measure Early Childhood Development in Large Scale Studies.

    Directory of Open Access Journals (Sweden)

    Marta Rubio-Codina

    Full Text Available In low- and middle-income countries (LIMCs, measuring early childhood development (ECD with standard tests in large scale surveys and evaluations of interventions is difficult and expensive. Multi-dimensional screeners and single-domain tests ('short tests' are frequently used as alternatives. However, their validity in these circumstances is unknown. We examined the feasibility, reliability, and concurrent validity of three multi-dimensional screeners (Ages and Stages Questionnaires (ASQ-3, Denver Developmental Screening Test (Denver-II, Battelle Developmental Inventory screener (BDI-2 and two single-domain tests (MacArthur-Bates Short-Forms (SFI and SFII, WHO Motor Milestones (WHO-Motor in 1,311 children 6-42 months in Bogota, Colombia. The scores were compared with those on the Bayley Scales of Infant and Toddler Development (Bayley-III, taken as the 'gold standard'. The Bayley-III was given at a center by psychologists; whereas the short tests were administered in the home by interviewers, as in a survey setting. Findings indicated good internal validity of all short tests except the ASQ-3. The BDI-2 took long to administer and was expensive, while the single-domain tests were quickest and cheapest and the Denver-II and ASQ-3 were intermediate. Concurrent validity of the multi-dimensional tests' cognitive, language, and fine motor scales with the corresponding Bayley-III scale was low below 19 months. However, it increased with age, becoming moderate-to-high over 30 months. In contrast, gross motor scales' concurrence was high under 19 months and then decreased. Of the single-domain tests, the WHO-Motor had high validity with gross motor under 16 months, and the SFI and SFII expressive scales showed moderate correlations with language under 30 months. Overall, the Denver-II was the most feasible and valid multi-dimensional test and the ASQ-3 performed poorly under 31 months. By domain, gross motor development had the highest concurrence

  6. Short-circuit tests of 1650 and 96 MVA transformers for 1300 MW french nuclear power plants

    International Nuclear Information System (INIS)

    Mailhot, M.

    1989-01-01

    Power evacuation and feeding of the auxiliaries directly from the 400 kV grid are sensitive points governing the security of 1300 MW PWR Nuclear Power Plants of the French Program. These two different functions are provided by two specific types of transformers. - Banks of 3 single-phase 550 MVA - 400 kV/20 kV transformers. - Three-phase 96 MVA - 400 kV / 3 x 6.8 kV transformers. These passive elements must have a never failing reliability and assure a continuous service in spite of electric, thermal and mechanical stresses that may occur during the lifetime of the power plant. Dielectric and thermal tests carried out in the manufacturers test floors insure these stresses withstand capabilities of transformers. In France, high short-circuit power for the 400 kV network added to often low impedance voltages for transformers impose on them very high stresses during short-circuits. Calculation and experimentation on scale or partial models are not sufficient to insure short-circuit currents withstand capabilities of transformers. The margin of uncertainty dependent on obligatory extrapolations for this kind of complex systems [steel, magnetic sheets, copper, oil, paper and transformerboard] can be reduced in a significant way only by real scale tests on prototypes. These tests that need both high power and voltage cannot be performed in manufacturers test floors. So, in France they are carried out at the EDF Les Renardieres Laboratory. Following paper deals with SHELL TYPE TRANSFORMERS which, particularly thanks to their interleaved rectangular windings display a great resistance to short-circuit stresses

  7. Detection of optic nerve atrophy following a single episode of unilateral optic neuritis by MRI using a fat-saturated short-echo fast FLAIR sequence

    International Nuclear Information System (INIS)

    Hickman, S.J.; Brex, P.A.; Silver, N.C.; Barker, G.J.; Miller, D.H.; Brierley, C.M.H.; Compston, D.A.S.; Scolding, N.J.; Moseley, I.F.; Plant, G.T.

    2001-01-01

    We describe an MRI technique for quantifying optic nerve atrophy resulting from a single episode of unilateral optic neuritis. We imaged 17 patients, with a median time since onset of optic neuritis of 21 months (range 3-81 months), using a coronal-oblique fat-saturated short-echo fast fluid-attenuated inversion-recovery (sTE fFLAIR) sequence. The mean cross-sectional area of the intraorbital portion of the optic nerves was calculated by a blinded observer from five consecutive 3 mm slices from the orbital apex forwards using a semiautomated contouring technique and compared with data from 16 controls. The mean optic nerve area was 11.2mm 2 in the affected eye of the patients, 12.9mm 2 in the contralateral eye (P = 0.006 compared to the affected eye) and 12.8mm 2 in controls (P = 0.03 compared to the affected eyes). There was a significant negative correlation between disease duration and the size of the affected optic nerve (r = -0.59, P = 0.012). The measurement coefficient of variation was 4.8 %. The sTE fFLAIR sequence enables measurement of optic nerve area with sufficient reproducibility to show optic nerve atrophy following a single episode of unilateral optic neuritis. The correlation of increasing optic nerve atrophy with disease duration would be consistent with ongoing axonal loss in a persistently demyelinated lesion, or Wallerian degeneration following axonal damage during the acute inflammatory phase. (orig.)

  8. Use of short-term test systems for the prediction of the hazard represented by potential chemical carcinogens

    International Nuclear Information System (INIS)

    Glass, L.R.; Jones, T.D.; Easterly, C.E.; Walsh, P.J.

    1990-10-01

    It has been hypothesized that results from short-term bioassays will ultimately provide information that will be useful for human health hazard assessment. Historically, the validity of the short-term tests has been assessed using the framework of the epidemiologic/medical screens. In this context, the results of the carcinogen (long-term) bioassay is generally used as the standard. However, this approach is widely recognized as being biased and, because it employs qualitative data, cannot be used to assist in isolating those compounds which may represent a more significant toxicologic hazard than others. In contrast, the goal of this research is to address the problem of evaluating the utility of the short-term tests for hazard assessment using an alternative method of investigation. Chemicals were selected mostly from the list of carcinogens published by the International Agency for Research on Carcinogens (IARC); a few other chemicals commonly recognized as hazardous were included. Tumorigenicity and mutagenicity data on 52 chemicals were obtained from the Registry of Toxic Effects of Chemical Substances (RTECS) and were analyzed using a relative potency approach. The data were evaluated in a format which allowed for a comparison of the ranking of the mutagenic relative potencies of the compounds (as estimated using short-term data) vs. the ranking of the tumorigenic relative potencies (as estimated from the chronic bioassays). Although this was a preliminary investigation, it offers evidence that the short-term tests systems may be of utility in ranking the hazards represented by chemicals which may contribute to increased carcinogenesis in humans as a result of occupational or environmental exposures. 177 refs., 8 tabs

  9. Use of short-term test systems for the prediction of the hazard represented by potential chemical carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Glass, L.R.; Jones, T.D.; Easterly, C.E.; Walsh, P.J.

    1990-10-01

    It has been hypothesized that results from short-term bioassays will ultimately provide information that will be useful for human health hazard assessment. Historically, the validity of the short-term tests has been assessed using the framework of the epidemiologic/medical screens. In this context, the results of the carcinogen (long-term) bioassay is generally used as the standard. However, this approach is widely recognized as being biased and, because it employs qualitative data, cannot be used to assist in isolating those compounds which may represent a more significant toxicologic hazard than others. In contrast, the goal of this research is to address the problem of evaluating the utility of the short-term tests for hazard assessment using an alternative method of investigation. Chemicals were selected mostly from the list of carcinogens published by the International Agency for Research on Carcinogens (IARC); a few other chemicals commonly recognized as hazardous were included. Tumorigenicity and mutagenicity data on 52 chemicals were obtained from the Registry of Toxic Effects of Chemical Substances (RTECS) and were analyzed using a relative potency approach. The data were evaluated in a format which allowed for a comparison of the ranking of the mutagenic relative potencies of the compounds (as estimated using short-term data) vs. the ranking of the tumorigenic relative potencies (as estimated from the chronic bioassays). Although this was a preliminary investigation, it offers evidence that the short-term tests systems may be of utility in ranking the hazards represented by chemicals which may contribute to increased carcinogenesis in humans as a result of occupational or environmental exposures. 177 refs., 8 tabs.

  10. Acceptance test for the linear motion actuator for the scanning slit of the HIE-ISOLDE short diagnostic boxes

    CERN Document Server

    Cantero, E D; Bravin, E; Sosa, A

    2014-01-01

    We performed experimental tests to characterize the mechanical accuracy of a linear actuator designed by the company AVS for the movement of the scanning slit of the HIE-ISOLDE short diagnostic boxes. The mechanism consists of a linear actuator composed of two guiding rods and a lead screw, with a full stroke of 135 mm. A specially designed blade was mounted on the actuator and the transverse positioning of the blade was monitored with a camera-based optical system while moving the actuator at speeds of up to 10 mm/s. The repeatability of the positioning of the blade after several cycles around predefined positions was also measured. The results of the measurements and a general inspection of the device show that the proposed solution fulfils the specifications. A full prototype of short diagnostic box for the HIE-ISOLDE project can now be built for testing.

  11. Why wait if you can switch? A short term testing effect in cross-language recognition.

    NARCIS (Netherlands)

    Verkoeijen, Peter; Bouwmeester, Samantha; Camp, Gino

    2018-01-01

    Taking a memory test after an initial study phase produces better long-term retention than restudying the items, a phenomenon known as the testing effect. We propose that this effect emerges because testing strengthens semantic features of items’ memory traces, whereas restudying strengthens surface

  12. Effects of Two Short-Term Desensitization Methods in the Treatment of Test Anxiety

    Science.gov (United States)

    Richardson, Frank C.; Suinn, Richard M.

    1974-01-01

    Accelerated massed desensitization and anxiety management training were compared with standard systematic desensitization in terms of reducing self-reported test anxiety in high test-anxious college students. All three treatments significantly reduced test anxiety as compared with a waiting list control group. (Author)

  13. MK-801 and memantine act differently on short-term memory tested with different time-intervals in the Morris water maze test.

    Science.gov (United States)

    Duda, Weronika; Wesierska, Malgorzata; Ostaszewski, Pawel; Vales, Karel; Nekovarova, Tereza; Stuchlik, Ales

    2016-09-15

    N-methyl-d-aspartate receptors (NMDARs) play a crucial role in spatial memory formation. In neuropharmacological studies their functioning strongly depends on testing conditions and the dosage of NMDAR antagonists. The aim of this study was to assess the immediate effects of NMDAR block by (+)MK-801 or memantine on short-term allothetic memory. Memory was tested in a working memory version of the Morris water maze test. In our version of the test, rats underwent one day of training with 8 trials, and then three experimental days when rats were injected intraperitoneally with low- 5 (MeL), high - 20 (MeH) mg/kg memantine, 0.1mg/kg MK-801 or 1ml/kg saline (SAL) 30min before testing, for three consecutive days. On each experimental day there was just one acquisition and one test trial, with an inter-trial interval of 5 or 15min. During training the hidden platform was relocated after each trial and during the experiment after each day. The follow-up effect was assessed on day 9. Intact rats improved their spatial memory across the one training day. With a 5min interval MeH rats had longer latency then all rats during retrieval. With a 15min interval the MeH rats presented worse working memory measured as retrieval minus acquisition trial for path than SAL and MeL and for latency than MeL rats. MK-801 rats had longer latency than SAL during retrieval. Thus, the high dose of memantine, contrary to low dose of MK-801 disrupts short-term memory independent on the time interval between acquisition and retrieval. This shows that short-term memory tested in a working memory version of water maze is sensitive to several parameters: i.e., NMDA receptor antagonist type, dosage and the time interval between learning and testing. Copyright © 2016. Published by Elsevier B.V.

  14. Next-generation sequencing for genetic testing of familial colorectal cancer syndromes.

    Science.gov (United States)

    Simbolo, Michele; Mafficini, Andrea; Agostini, Marco; Pedrazzani, Corrado; Bedin, Chiara; Urso, Emanuele D; Nitti, Donato; Turri, Giona; Scardoni, Maria; Fassan, Matteo; Scarpa, Aldo

    2015-01-01

    Genetic screening in families with high risk to develop colorectal cancer (CRC) prevents incurable disease and permits personalized therapeutic and follow-up strategies. The advancement of next-generation sequencing (NGS) technologies has revolutionized the throughput of DNA sequencing. A series of 16 probands for either familial adenomatous polyposis (FAP; 8 cases) or hereditary nonpolyposis colorectal cancer (HNPCC; 8 cases) were investigated for intragenic mutations in five CRC familial syndromes-associated genes (APC, MUTYH, MLH1, MSH2, MSH6) applying both a custom multigene Ion AmpliSeq NGS panel and conventional Sanger sequencing. Fourteen pathogenic variants were detected in 13/16 FAP/HNPCC probands (81.3 %); one FAP proband presented two co-existing pathogenic variants, one in APC and one in MUTYH. Thirteen of these 14 pathogenic variants were detected by both NGS and Sanger, while one MSH2 mutation (L280FfsX3) was identified only by Sanger sequencing. This is due to a limitation of the NGS approach in resolving sequences close or within homopolymeric stretches of DNA. To evaluate the performance of our NGS custom panel we assessed its capability to resolve the DNA sequences corresponding to 2225 pathogenic variants reported in the COSMIC database for APC, MUTYH, MLH1, MSH2, MSH6. Our NGS custom panel resolves the sequences where 2108 (94.7 %) of these variants occur. The remaining 117 mutations reside inside or in close proximity to homopolymer stretches; of these 27 (1.2 %) are imprecisely identified by the software but can be resolved by visual inspection of the region, while the remaining 90 variants (4.0 %) are blind spots. In summary, our custom panel would miss 4 % (90/2225) of pathogenic variants that would need a small set of Sanger sequencing reactions to be solved. The multiplex NGS approach has the advantage of analyzing multiple genes in multiple samples simultaneously, requiring only a reduced number of Sanger sequences to resolve

  15. Testing for Unit Roots in Small Panels with Short-run and Long-run Cross-sectional Dependencies

    OpenAIRE

    Yoosoon Chang; Wonho Song

    2009-01-01

    An IV approach, using as instruments non-linear transformations of the lagged levels, is explored to test for unit roots in panels with general dependency and heterogeneity across cross-sectional units. We allow not only for the cross-sectional dependencies of innovations, but also for the presence of co-integration across cross-sectional levels. Unbalanced panels and panels with differing individual short-run dynamics and cross-sectionally related dynamics are also permitted. We also more ca...

  16. A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

    Science.gov (United States)

    Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

    2014-01-01

    The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

  17. Signal processing of data from short sample tests for the projection of conductor performance in ITER magnets

    International Nuclear Information System (INIS)

    Martovetsky, Nicolai

    2008-01-01

    Qualification of the ITER conductor is absolutely necessary. Testing large scale conductors is expensive and time-consuming. To test 3-4 m long straight samples in a bore of a split solenoid is a relatively economical way in comparison with the fabrication of a coil to be tested in a bore of a background field solenoid. However, testing short samples may give ambiguous results due to different constraints in current redistribution in the cable or other end effects which are not present in the large magnet. This paper discusses the processes taking place in the ITER conductor, conditions when conductor performance could be distorted and possible signal processing to deduce the behaviour of ITER conductors in ITER magnets from the test data

  18. The test facility for the short prototypes of the LHC superconducting magnets

    International Nuclear Information System (INIS)

    Delsolaro, W. Venturini; Arn, A.; Bottura, L.; Giloux, C.; Mompo, R.; Siemko, A.; Walckiers, L.

    2002-01-01

    The LHC development program relies on cryogenic tests of prototype and model magnets. This vigorous program is pursued in a dedicated test facility based on several vertical cryostats working at superfluid helium temperatures. The performance of the facility is detailed. Goals and test equipment for currently performed studies are reviewed: quench analysis and magnet protection studies, measurement of the field quality, test of ancillary electrical equipment like diodes and busbars. The paper covers the equipment available for tests of prototypes and some special series of LHC magnets to come

  19. The test facility for the short prototypes of the LHC superconducting magnets

    Science.gov (United States)

    Delsolaro, W. Venturini; Arn, A.; Bottura, L.; Giloux, C.; Mompo, R.; Siemko, A.; Walckiers, L.

    2002-05-01

    The LHC development program relies on cryogenic tests of prototype and model magnets. This vigorous program is pursued in a dedicated test facility based on several vertical cryostats working at superfluid helium temperatures. The performance of the facility is detailed. Goals and test equipment for currently performed studies are reviewed: quench analysis and magnet protection studies, measurement of the field quality, test of ancillary electrical equipment like diodes and busbars. The paper covers the equipment available for tests of prototypes and some special series of LHC magnets to come.

  20. Comparison of the clonidine test with the insulin tolerance test in the evaluation of patients with short stature

    International Nuclear Information System (INIS)

    Batista, M.C.

    1986-01-01

    Thirty one patients aged 2.9 to 17.5 years, with heights from 1.3 to 85 standard deviations below the mean for age and sex, are studied. Two GH provocative tests are done: (1) insulin tolerance test (ITT): intravenous regular insulin 0.1 U/kg body weight; (2) clonidine test (CLOT): oral clonidine 0.0375 mg/m 2 surface area. Serum GH is measured by a radioimmunoassay method developed in the laboratory and calibrated against a reference preparation provided by the National Institutes of Health. (M.A.C.) [pt

  1. Magnetic resonance imaging of pelvic entheses - a systematic comparison between short tau inversion recovery (STIR) and T1-weighted, contrast-enhanced, fat-saturated sequences

    International Nuclear Information System (INIS)

    Klang, Eyal; Aharoni, Dvora; Rimon, Uri; Eshed, Iris; Hermann, Kay-Geert; Herman, Amir; Shazar, Nachshon

    2014-01-01

    To assess the contribution of contrast material in detecting and evaluating enthesitis of pelvic entheses by MRI. Sixty-seven hip or pelvic 1.5-T MRIs (30:37 male:female, mean age: 53 years) were retrospectively evaluated for the presence of hamstring and gluteus medius (GM) enthesitis by two readers (a resident and an experienced radiologist). Short tau inversion recovery (STIR) and T1-weighted pre- and post-contrast (T1+Gd) images were evaluated by each reader at two sessions. A consensus reading of two senior radiologists was regarded as the gold standard. Clinical data was retrieved from patients' referral form and medical files. Cohen's kappa was used for intra- and inter-observer agreement calculation. Diagnostic properties were calculated against the gold standard reading. A total of 228 entheses were evaluated. Gold standard analysis diagnosed 83 (36 %) enthesitis lesions. Intra-reader reliability for the experienced reader was significantly (p = 0.0001) higher in the T1+Gd images compared to the STIR images (hamstring: k = 0.84/0.45, GM: k = 0.84/0.47). Sensitivity and specificity increased from 0.74/0.8 to 0.87/0.9 in the STIR images and T1+Gd sequences. Intra-reader reliability for the inexperienced reader was lower (p > 0.05). Evidence showing that contrast material improves the reliability, sensitivity, and specificity of detecting enthesitis supports its use in this setting. (orig.)

  2. Testing the effect of a short cheap talk script in choice experiments

    DEFF Research Database (Denmark)

    Ladenburg, Jacob; Dahlgaard, Jens Olav; Bonnichsen, Ole

    as hypothetical bias. The present paper attempts to frame the description of the hypothetical market so as to induce more “true market behaviour” in the respondents by including a short Cheap Talk script. The script informs respondents that in similar studies using stated preference methods, people have...... to be a preference mover, but does not affect preferences significantly. Significant effects are found when relating the effect of the Cheap Talk script to the cost levels of the alternatives, in that female respondents are found to choose higher cost alternatives less frequently when presented with the Cheap Talk...

  3. Testing the effect of a short cheap talk script in choice experiments

    DEFF Research Database (Denmark)

    Ladenburg, Jacob; Bonnichsen, Ole; Dahlgaard, Jens Olav

    2011-01-01

    as hypothetical bias. The present paper attempts to frame the description of the hypothetical market so as to induce more “true market behaviour” in the respondents by including a short Cheap Talk script. The script informs respondents that in similar studies using stated preference methods, people have...... the demand for visual impact mitigation, but does not affect preferences significantly. Significant effects are found when relating the effect of the Cheap Talk script to the cost levels of the alternatives, in that female respondents are found to choose higher cost alternatives less frequently when...

  4. A consistency test of white dwarf and main sequence ages: NGC 6791

    Directory of Open Access Journals (Sweden)

    Córsico A.H.

    2013-03-01

    Full Text Available NGC 6791 is an open cluster that it is so close to us that can be imaged down to very faint luminosities. The main sequence turn-off age (∼8 Gyr and the age derived from the cut-off of the white dwarf luminosity function (∼6 Gyr were found to be significantly different. Here we demonstrate that the origin of this age discrepancy lies in an incorrect evaluation of the white dwarf cooling ages, and we show that when the relevant physical separation processes are included in the calculation of white dwarf sequences both ages are coincident.

  5. Structural identification of short/middle span bridges by rapid impact testing: theory and verification

    International Nuclear Information System (INIS)

    Zhang, Jian; Wu, Z S; Zhang, Q Q; Guo, S L; Xu, D W

    2015-01-01

    A structural strain flexibility identification method by processing the multiple-reference impact testing data is proposed. First, a kind of novel long-gauge fiber optic sensor is developed for structural macro-strain monitoring. Second, the multiple-reference impact testing technology is employed, during which both the impacting force and structural strain responses are measured. The impact testing technology has unique merit because it is able to extract exact structural frequency response functions (FRFs), while other test methods, for instance ambient tests, can only output the FRFs with scaled magnitudes. Most importantly, the originality of the article is that a method of identifying the structural strain flexibility characteristic from the impact test data has been proposed, which is useful for structural static strain prediction and capacity evaluation. Examples of a six meter simple supported beam and a multiple-span continuous beam bridge have successfully verified the effectiveness of the proposed method. (paper)

  6. Structural identification of short/middle span bridges by rapid impact testing: theory and verification

    Science.gov (United States)

    Zhang, Jian; Zhang, Q. Q.; Guo, S. L.; Xu, D. W.; Wu, Z. S.

    2015-06-01

    A structural strain flexibility identification method by processing the multiple-reference impact testing data is proposed. First, a kind of novel long-gauge fiber optic sensor is developed for structural macro-strain monitoring. Second, the multiple-reference impact testing technology is employed, during which both the impacting force and structural strain responses are measured. The impact testing technology has unique merit because it is able to extract exact structural frequency response functions (FRFs), while other test methods, for instance ambient tests, can only output the FRFs with scaled magnitudes. Most importantly, the originality of the article is that a method of identifying the structural strain flexibility characteristic from the impact test data has been proposed, which is useful for structural static strain prediction and capacity evaluation. Examples of a six meter simple supported beam and a multiple-span continuous beam bridge have successfully verified the effectiveness of the proposed method.

  7. Concreteness effects in short-term memory: a test of the item-order hypothesis.

    Science.gov (United States)

    Roche, Jaclynn; Tolan, G Anne; Tehan, Gerald

    2011-12-01

    The following experiments explore word length and concreteness effects in short-term memory within an item-order processing framework. This framework asserts order memory is better for those items that are relatively easy to process at the item level. However, words that are difficult to process benefit at the item level for increased attention/resources being applied. The prediction of the model is that differential item and order processing can be detected in episodic tasks that differ in the degree to which item or order memory are required by the task. The item-order account has been applied to the word length effect such that there is a short word advantage in serial recall but a long word advantage in item recognition. The current experiment considered the possibility that concreteness effects might be explained within the same framework. In two experiments, word length (Experiment 1) and concreteness (Experiment 2) are examined using forward serial recall, backward serial recall, and item recognition. These results for word length replicate previous studies showing the dissociation in item and order tasks. The same was not true for the concreteness effect. In all three tasks concrete words were better remembered than abstract words. The concreteness effect cannot be explained in terms of an item-order trade off. PsycINFO Database Record (c) 2011 APA, all rights reserved.

  8. X-38 Drop Model: Landing Sequence Collage from Cessna Drop Test

    Science.gov (United States)

    1995-01-01

    This sequence of photographs shows a 4-foot-long model of NASA's X-38 gliding to earth after being dropped from a Cessna aircraft in late 1995. The model was used to test the ram-air parafoil landing system, which could allow for accurate and controlled landings of an emergency Crew Return Vehicle spacecraft returning to earth. The X-38 Crew Return Vehicle (CRV) research project is designed to develop the technology for a prototype emergency crew return vehicle, or lifeboat, for the International Space Station. The project is also intended to develop a crew return vehicle design that could be modified for other uses, such as a joint U.S. and international human spacecraft that could be launched on the French Ariane-5 Booster. The X-38 project is using available technology and off-the-shelf equipment to significantly decrease development costs. Original estimates to develop a capsule-type crew return vehicle were estimated at more than $2 billion. X-38 project officials have estimated that development costs for the X-38 concept will be approximately one quarter of the original estimate. Off-the-shelf technology is not necessarily 'old' technology. Many of the technologies being used in the X-38 project have never before been applied to a human-flight spacecraft. For example, the X-38 flight computer is commercial equipment currently used in aircraft and the flight software operating system is a commercial system already in use in many aerospace applications. The video equipment for the X-38 is existing equipment, some of which has already flown on the space shuttle for previous NASA experiments. The X-38's primary navigational equipment, the Inertial Navigation System/Global Positioning System, is a unit already in use on Navy fighters. The X-38 electromechanical actuators come from previous joint NASA, U.S. Air Force, and U.S. Navy research and development projects. Finally, an existing special coating developed by NASA will be used on the X-38 thermal tiles to

  9. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE – binding linear epitopes of allergens

    Directory of Open Access Journals (Sweden)

    Peijnenburg Ad ACM

    2002-12-01

    Full Text Available Abstract Background Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acids are further screened for the presence of potential linear IgE-epitopes. This double track approach involves the use of literature data on IgE-epitopes and an antigenicity prediction algorithm. Results Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. Twenty-two transgenic proteins showed positive results of six- or seven-contiguous amino acids length. Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase and allergenic proteins could be identified as (part of potential linear epitopes. Conclusion Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. Most identical stretches are likely to be false positives. As shown in this study, identical stretches can be further screened for relevance by comparison with linear IgE-binding epitopes described in literature. In the absence of literature data on epitopes, antigenicity prediction by computer aids to select potential antibody binding sites that will need verification of IgE binding by sera binding tests. Finally, the positive outcomes of this approach warrant further clinical testing for potential allergenicity.

  10. The role of next generation sequencing for the development and testing of veterinary biologics

    Science.gov (United States)

    Next generation sequencing technology has become widely available and it offers many new opportunities in vaccine technology. Both human and veterinary medicine has numerous examples of adventitious agents being found in live vaccines. In veterinary medicine a continuing trend is the use of viral ...

  11. Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions

    Directory of Open Access Journals (Sweden)

    Ivone U. S. Leong

    2014-06-01

    Full Text Available Sudden cardiac death in people between the ages of 1–40 years is a devastating event and is frequently caused by several heritable cardiac disorders. These disorders include cardiac ion channelopathies, such as long QT syndrome, catecholaminergic polymorphic ventricular tachycardia and Brugada syndrome and cardiomyopathies, such as hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. Through careful molecular genetic evaluation of DNA from sudden death victims, the causative gene mutation can be uncovered, and the rest of the family can be screened and preventative measures implemented in at-risk individuals. The current screening approach in most diagnostic laboratories uses Sanger-based sequencing; however, this method is time consuming and labour intensive. The development of massively parallel sequencing has made it possible to produce millions of sequence reads simultaneously and is potentially an ideal approach to screen for mutations in genes that are associated with sudden cardiac death. This approach offers mutation screening at reduced cost and turnaround time. Here, we will review the current commercially available enrichment kits, massively parallel sequencing (MPS platforms, downstream data analysis and its application to sudden cardiac death in a diagnostic environment.

  12. Comparison of short-term estrogenicity tests for identification of hormone-disrupting chemicals

    DEFF Research Database (Denmark)

    Andersen, H R; Andersson, A M; Arnold, S F

    1999-01-01

    induced a strong estrogenic response in all test systems. Colchicine caused cytotoxicity only. Bisphenol A induced an estrogenic response in all assays. The results obtained for the remaining test compounds--tamoxifen, ICI 182.780, testosterone, bisphenol A dimethacrylate, 4-n-octylphenol, 4-n...

  13. A Short Test for the Assessment of Basic Knowledge in Psychology

    Science.gov (United States)

    Peter, Johannes; Leichner, Nikolas; Mayer, Anne-Kathrin; Krampen, Günter

    2015-01-01

    This paper reports the development of a fixed-choice test for the assessment of basic knowledge in psychology, for use with undergraduate as well as graduate students. Test content is selected based on a core concepts approach and includes a sample of concepts which are indexed most frequently in common introductory psychology textbooks. In a…

  14. Short-term practice effects and variability in cognitive testing in a healthy elderly population

    DEFF Research Database (Denmark)

    Krenk, L.; Rasmussen, L.S.; Siersma, V.

    2012-01-01

    BACKGROUND: Cognitive decline in the elderly is a subject of intense focus. However, there is a lack of consensus regarding definition of significant decline in connection with repeated testing and the interpretation of cognitive tests results must take into account the practice effect...

  15. Parallel algorithms for testing finite state machines:Generating UIO sequences

    OpenAIRE

    Hierons, RM; Turker, UC

    2016-01-01

    This paper describes an efficient parallel algorithm that uses many-core GPUs for automatically deriving Unique Input Output sequences (UIOs) from Finite State Machines. The proposed algorithm uses the global scope of the GPU's global memory through coalesced memory access and minimises the transfer between CPU and GPU memory. The results of experiments indicate that the proposed method yields considerably better results compared to a single core UIO construction algorithm. Our algorithm is s...

  16. Whole body sodium MRI at 3T using an asymmetric birdcage resonator and short echo time sequence: first images of a male volunteer

    Science.gov (United States)

    Wetterling, Friedrich; Corteville, Dominique M.; Kalayciyan, Raffi; Rennings, Andreas; Konstandin, Simon; Nagel, Armin M.; Stark, Helmut; Schad, Lothar R.

    2012-07-01

    Sodium magnetic resonance imaging (23Na MRI) is a non-invasive technique which allows spatial resolution of the tissue sodium concentration (TSC) in the human body. TSC measurements could potentially serve to monitor early treatment success of chemotherapy on patients who suffer from whole body metastases. Yet, the acquisition of whole body sodium (23Na) images has been hampered so far by the lack of large resonators and the extremely low signal-to-noise ratio (SNR) achieved with existing resonator systems. In this study, a 23Na resonator was constructed for whole body 23Na MRI at 3T comprising of a 16-leg, asymmetrical birdcage structure with 34 cm height, 47.5 cm width and 50 cm length. The resonator was driven in quadrature mode and could be used either as a transceiver resonator or, since active decoupling was included, as a transmit-only resonator in conjunction with a receive-only (RO) surface resonator. The relative B1-field profile was simulated and measured on phantoms, and 3D whole body 23Na MRI data of a healthy male volunteer were acquired in five segments with a nominal isotropic resolution of (6 × 6 × 6) mm3 and a 10 min acquisition time per scan. The measured SNR values in the 23Na-MR images varied from 9 ± 2 in calf muscle, 15 ± 2 in brain tissue, 23 ± 2 in the prostate and up to 42 ± 5 in the vertebral discs. Arms, legs, knees and hands could also be resolved with applied resonator and short time-to-echo (TE) (0.5 ms) radial sequence. Up to fivefold SNR improvement was achieved through combining the birdcage with local RO surface coil. In conclusion, 23Na MRI of the entire human body provides sub-cm spatial resolution, which allows resolution of all major human body parts with a scan time of less than 60 min.

  17. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Science.gov (United States)

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  18. Routine blood tests are associated with short term mortality and can improve emergency department triage

    DEFF Research Database (Denmark)

    Kristensen, Michael; Iversen, Anne Kristine Servais; Gerds, Thomas Alexander

    2017-01-01

    BACKGROUND: Prioritization of acutely ill patients in the Emergency Department remains a challenge. We aimed to evaluate whether routine blood tests can predict mortality in unselected patients in an emergency department and to compare risk prediction with a formalized triage algorithm. METHODS...... registration. Multiple logistic regressions were used to predict 30-day mortality. Validation was performed by applying the regression models on the 2013 validation cohort. RESULTS: Thirty-day mortality was 5.3%. The routine blood tests had a significantly stronger discriminative value on 30-day mortality...... compared to the formalized triage (AUC 88.1 [85.7;90.5] vs. 63.4 [59.1;67.5], p blood tests was able to identify a larger number of low risk patients (n = 2100, 30-day mortality 0.1% [95% CI 0.0;0.3%]) compared to formalized triage (n = 1591, 2.8% [95% CI 2...

  19. Prediction of long time creep rupture properties of welded joints using the results of short duration creep crack incubation tests

    Energy Technology Data Exchange (ETDEWEB)

    Hosseini, E.

    2013-07-01

    This dissertation submitted to the Swiss Federal Institute of Technology ETH in Zurich examines the applicability of the LICON methodology for the prediction of long-time creep rupture strength of a dissimilar metal weld. The LICON methodology is an approach for predicting the lifetime of materials under creep loading conditions. It predicts long-time uniaxial creep strength using the results from several short duration creep crack incubation tests in conjunction with the outcome of a mechanical analysis on the test-piece. This study has re-examined the previous application of the LICON methodology for 9%Cr and 1CrMoV steels. It has shown that application of the original Lion method (based on reference stress solutions) for certain materials is not appropriate. This study therefore proposes a new development for the Lion approach which uses finite-element analysis to account for the generated multiaxial stress states within welded uniaxial test-pieces.

  20. Prediction of long time creep rupture properties of welded joints using the results of short duration creep crack incubation tests

    International Nuclear Information System (INIS)

    Hosseini, E.

    2013-01-01

    This dissertation submitted to the Swiss Federal Institute of Technology ETH in Zurich examines the applicability of the LICON methodology for the prediction of long-time creep rupture strength of a dissimilar metal weld. The LICON methodology is an approach for predicting the lifetime of materials under creep loading conditions. It predicts long-time uniaxial creep strength using the results from several short duration creep crack incubation tests in conjunction with the outcome of a mechanical analysis on the test-piece. This study has re-examined the previous application of the LICON methodology for 9%Cr and 1CrMoV steels. It has shown that application of the original Lion method (based on reference stress solutions) for certain materials is not appropriate. This study therefore proposes a new development for the Lion approach which uses finite-element analysis to account for the generated multiaxial stress states within welded uniaxial test-pieces

  1. Development and testing of an innovative short-term large wind ramp forecasting system

    Energy Technology Data Exchange (ETDEWEB)

    Zack, J.W. [AWS Truepower LLC, Troy, NY (United States)

    2010-07-01

    This PowerPoint presentation discussed a ramp forecasting tool designed for use in a region of Texas with a high wind-generating capacity. Large system-wide ramps frequently occur in the region, and curtailments are common due to transmission constraints. The average hourly load of the power system is 32,101 MW. Wind power capacity in the region is 9382 MW. However, actual production rarely exceeds 6500 MW due to the curtailments. The short-term ramp forecasting tool was designed to aid in grid management decisions for the 0-6 hour ahead period as well as to address issues related to wind farm time series data and the lack of situational awareness information. The tool provided rapid updates for grid point wind analysis with feature detection and tracking algorithms and a rapid update cycle model. The tool also featured a suite of web-based applications that included deterministic ramp even forecasts, power production time series forecasts, and situational awareness products that are updated every 15 minutes. A performance evaluation study of the tool was provided. tabs., figs.

  2. The use of standardised short-term and working memory tests in aphasia research: a systematic review.

    Science.gov (United States)

    Murray, Laura; Salis, Christos; Martin, Nadine; Dralle, Jenny

    2018-04-01

    Impairments of short-term and working memory (STM, WM), both verbal and non-verbal, are ubiquitous in aphasia. Increasing interest in assessing STM and WM in aphasia research and clinical practice as well as a growing evidence base of STM/WM treatments for aphasia warrant an understanding of the range of standardised STM/WM measures that have been utilised in aphasia. To date, however, no previous systematic review has focused on aphasia. Accordingly, the goals of this systematic review were: (1) to identify standardised tests of STM and WM utilised in the aphasia literature, (2) to evaluate critically the psychometric strength of these tests, and (3) to appraise critically the quality of the investigations utilising these tests. Results revealed that a very limited number of standardised tests, in the verbal and non-verbal domains, had robust psychometric properties. Standardisation samples to elicit normative data were often small, and most measures exhibited poor validity and reliability properties. Studies using these tests inconsistently documented demographic and aphasia variables essential to interpreting STM/WM test outcomes. In light of these findings, recommendations are provided to foster, in the future, consistency across aphasia studies and confidence in STM/WM tests as assessment and treatment outcome measures.

  3. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

    DEFF Research Database (Denmark)

    Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer

    2013-01-01

    -genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures. Methods: Antimicrobial susceptibility tests were performed...... to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella...

  4. Measuring Attending Behavior and Short-Term Memory with Knox's Cube Test.

    Science.gov (United States)

    Stone, Mark H.; Wright, Benjamin D.

    1983-01-01

    A new revision was developed using Rasch psychometric techniques to build a Knox's Cube Test (KCT) variable and item bank using the tapping series from all previous editions. The report forms developed give a clear picture of the subject's performance set in a context that is both normative and criterion. (Author/BW)

  5. Short term creep small punch testing of P91 and P92 steels,

    Czech Academy of Sciences Publication Activity Database

    Dymáček, Petr

    2011-01-01

    Roč. 465, - (2011), s. 179-182 ISSN 1013-9826. [Materials Structure & Micromechanics of Fracture 6. Brno, 28.6.2010-30.6,2010] R&D Projects: GA AV ČR(CZ) IAA200410801 Institutional research plan: CEZ:AV0Z20410507 Keywords : creep * small punch test * chromium steel Subject RIV: JG - Metallurgy

  6. A Short Submaximal test to determine the fatigue threshold of knee extensors in young men

    NARCIS (Netherlands)

    de Ruiter, C.J.; Hamacher, P.; Wolfs, B.G.A.

    Purpose Recently, a fatigue threshold obtained during submaximal repetitive isometric knee extensor contractions was related to VO 2max measured during cycling and to exercise endurance. However, test duration is quite long (20-30 min in young people) to be of practical and possibly clinical use.

  7. A comparison of computerized adaptive testing and fixed-length short forms for the Prosthetic Limb Users Survey of Mobility (PLUS-MTM).

    Science.gov (United States)

    Amtmann, Dagmar; Bamer, Alyssa M; Kim, Jiseon; Bocell, Fraser; Chung, Hyewon; Park, Ryoungsun; Salem, Rana; Hafner, Brian J

    2017-09-01

    New health status instruments can be administered by computerized adaptive test or short forms. The Prosthetic Limb Users Survey of Mobility (PLUS-M TM ) is a self-report measure of mobility for prosthesis users with lower limb loss. This study used the PLUS-M to examine advantages and disadvantages of computerized adaptive test and short forms. To compare scores obtained from computerized adaptive test to scores obtained from fixed-length short forms (7-item and 12-item) in order to provide guidance to researchers and clinicians on how to select the best form of administration for different uses. Cross-sectional, observational study. Individuals with lower limb loss completed the PLUS-M by computerized adaptive test and short forms. Administration time, correlations between the scores, and standard errors were compared. Scores and standard errors from the computerized adaptive test, 7-item short form, and 12-item short form were highly correlated and all forms of administration were efficient. Computerized adaptive test required less time to administer than either paper or electronic short forms; however, time savings were minimal compared to the 7-item short form. Results indicate that the PLUS-M computerized adaptive test is most efficient, and differences in scores between administration methods are minimal. The main advantage of the computerized adaptive test was more reliable scores at higher levels of mobility compared to short forms. Clinical relevance Health-related item banks, like the Prosthetic Limb Users Survey of Mobility (PLUS-M TM ), can be administered by computerized adaptive testing (CAT) or as fixed-length short forms (SFs). Results of this study will help clinicians and researchers decide whether they should invest in a CAT administration system or whether SFs are more appropriate.

  8. Influence of test tube material on subcooled flow boiling critical heat flux in short vertical tube

    International Nuclear Information System (INIS)

    Hata, Koichi; Shiotsu, Masahiro; Noda, Nobuaki

    2007-01-01

    The steady state subcooled flow boiling critical heat flux (CHF) for the flow velocities (u=4.0 to 13.3 m/s), the inlet subcoolings (ΔT sub,in =48.6 to 154.7 K), the inlet pressure (P in =735.2 to 969.0 kPa) and the increasing heat input (Q 0 exp(t/τ), τ=10, 20 and 33.3 s) are systematically measured with the experimental water loop. The 304 Stainless Steel (SUS304) test tube of inner diameter (d=6 mm), heated length (L=66 mm) and L/d=11 with the inner surface of rough finished (Surface roughness, Ra=3.18 μm), the Cupro Nickel (Cu-Ni 30%) test tube of d=6 mm, L=60 mm and L/d=10 with Ra=0.18 μm and the Platinum (Pt) test tubes of d=3 and 6 mm, L=66.5 and 69.6 mm, and L/d=22.2 and 11.6 respectively with Ra=0.45 μm are used in this work. The CHF data for the SUS304, Cu-Ni 30% and Pt test tubes were compared with SUS304 ones for the wide ranges of d and L/d previously obtained and the values calculated by the authors' published steady state CHF correlations against outlet and inlet subcoolings. The influence of the test tube material on CHF is investigated into details and the dominant mechanism of subcooled flow boiling critical heat flux is discussed. (author)

  9. Influence of Test Tube Material on Subcooled Flow Boiling Critical Heat Flux in Short Vertical Tube

    International Nuclear Information System (INIS)

    Koichi Hata; Masahiro Shiotsu; Nobuaki Noda

    2006-01-01

    The steady state subcooled flow boiling critical heat flux (CHF) for the flow velocities (u = 4.0 to 13.3 m/s), the inlet subcooling (ΔT sub,in = 48.6 to 154.7 K), the inlet pressure (P in = 735.2 to 969.0 kPa) and the increasing heat input (Q 0 exp(t/t), t = 10, 20 and 33.3 s) are systematically measured with the experimental water loop. The 304 Stainless Steel (SUS304) test tubes of inner diameters (d = 6 mm), heated lengths (L = 66 mm) and L/d = 11 with the inner surface of rough finished (Surface roughness, R a = 3.18 μm), the Cupro Nickel (Cu-Ni 30%) test tubes of d = 6 mm, L = 60 mm and L/d = 10 with R a = 0.18 μm and the Platinum (Pt) test tubes of d = 3 and 6 mm, L = 66.5 and 69.6 mm, and L/d 22.2 and 11.6 respectively with R a = 0.45 μm are used in this work. The CHF data for the SUS304, Cu-Ni 30% and Pt test tubes were compared with SUS304 ones for the wide ranges of d and L/d previously obtained and the values calculated by the authors' published steady state CHF correlations against outlet and inlet subcooling. The influence of the test tube material on CHF is investigated into details and the dominant mechanism of subcooled flow boiling critical heat flux is discussed. (authors)

  10. Application of rat mast cell incubates as a possible short-time test for sensitizing occupational chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Diel, F.; Neidhart, B.; Opree, W.

    1981-08-01

    The direct action of sensitizing occupational chemicals (formaldehyde, phenol, phenylhydrazine, p-aminophenol) on rat mast cells was investigated by determination of histamine using HPLC separation and fluorimetric detection. It turned out that dispersed mast cells from immunized and non-immunized Wistar-rats are more sensitive than small-cut lung tissue slices. Passive cutaneous anaphylaxis was negative after a fortnight sensitizing experiment with the here described occupational chemicals. Short-time tests with rat mast cells reflect anaphylactoid response and are suitable for the screening of sensitizing chemicals.

  11. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    There are nearly 7000 rare diseases that have been reported in the world. Although most of them occur with a frequency of less than one in 2000, in total about 6% of the population suffers from rare diseases. These rare diseases are often caused by changes in genes, which is currently lack of eff...... diseases and monogenetic diseases in a noninvasively manner. The new approach has great potential to be wildly used in the worldwide with the decreasing in sequencing costs, and therefore play an incredible role to prevent rare diseases....

  12. An Exponential Combination Procedure for Set-Based Association Tests in Sequencing Studies

    OpenAIRE

    Chen, Lin S.; Hsu, Li; Gamazon, Eric R.; Cox, Nancy J.; Nicolae, Dan L.

    2012-01-01

    State-of-the-art next-generation-sequencing technologies can facilitate in-depth explorations of the human genome by investigating both common and rare variants. For the identification of genetic factors that are associated with disease risk or other complex phenotypes, methods have been proposed for jointly analyzing variants in a set (e.g., all coding SNPs in a gene). Variants in a properly defined set could be associated with risk or phenotype in a concerted fashion, and by accumulating in...

  13. Aging irradiation of polymers. Dose-rate and test sequence influence

    International Nuclear Information System (INIS)

    Alba, C.; Carlin, F.; Chenion, J.; Lemaire, F.; Le Meur, M.; Petitjean, M.

    1984-05-01

    This work brings up results of the irradiation dose-rate influence on mechanical and electrical properties of technical polymer materials evolution. Polymer samples were subjected to 3.3.10 -2 Gy.s -1 and 2.8.10 -1 Gy.s -1 dose-rate. Heat and radiation simultaneous action is usualy simulated sequentialy. The hardest simulation on the polymer is the sequence of irradiation followed by thermal aging not the reverse. This study was carried out on eight polymer materials among those used in the electrical appliances for P.W.R. nuclear power plants [fr

  14. Phenotypic silencing of cytoplasmic genes using sequence-specific double-stranded short interfering RNA and its application in the reverse genetics of wild type negative-strand RNA viruses

    Directory of Open Access Journals (Sweden)

    Barik Sailen

    2001-12-01

    Full Text Available Abstract Background Post-transcriptional gene silencing (PTGS by short interfering RNA has opened up new directions in the phenotypic mutation of cellular genes. However, its efficacy on non-nuclear genes and its effect on the interferon pathway remain unexplored. Since directed mutation of RNA genomes is not possible through conventional mutagenesis, we have tested sequence-specific 21-nucleotide long double-stranded RNAs (dsRNAs for their ability to silence cytoplasmic RNA genomes. Results Short dsRNAs were generated against specific mRNAs of respiratory syncytial virus, a nonsegmented negative-stranded RNA virus with a cytoplasmic life cycle. At nanomolar concentrations, the dsRNAs specifically abrogated expression of the corresponding viral proteins, and produced the expected mutant phenotype ex vivo. The dsRNAs did not induce an interferon response, and did not inhibit cellular gene expression. The ablation of the viral proteins correlated with the loss of the specific mRNAs. In contrast, viral genomic and antigenomic RNA, which are encapsidated, were not directly affected. Conclusions Synthetic inhibitory dsRNAs are effective in specific silencing of RNA genomes that are exclusively cytoplasmic and transcribed by RNA-dependent RNA polymerases. RNA-directed RNA gene silencing does not require cloning, expression, and mutagenesis of viral cDNA, and thus, will allow the generation of phenotypic null mutants of specific RNA viral genes under normal infection conditions and at any point in the infection cycle. This will, for the first time, permit functional genomic studies, attenuated infections, reverse genetic analysis, and studies of host-virus signaling pathways using a wild type RNA virus, unencumbered by any superinfecting virus.

  15. Five-Kilometers Time Trial: Preliminary Validation of a Short Test for Cycling Performance Evaluation.

    Science.gov (United States)

    Dantas, Jose Luiz; Pereira, Gleber; Nakamura, Fabio Yuzo

    2015-09-01

    The five-kilometer time trial (TT5km) has been used to assess aerobic endurance performance without further investigation of its validity. This study aimed to perform a preliminary validation of the TT5km to rank well-trained cyclists based on aerobic endurance fitness and assess changes of the aerobic endurance performance. After the incremental test, 20 cyclists (age = 31.3 ± 7.9 years; body mass index = 22.7 ± 1.5 kg/m(2); maximal aerobic power = 360.5 ± 49.5 W) performed the TT5km twice, collecting performance (time to complete, absolute and relative power output, average speed) and physiological responses (heart rate and electromyography activity). The validation criteria were pacing strategy, absolute and relative reliability, validity, and sensitivity. Sensitivity index was obtained from the ratio between the smallest worthwhile change and typical error. The TT5km showed high absolute (coefficient of variation 0.95) reliability of performance variables, whereas it presented low reliability of physiological responses. The TT5km performance variables were highly correlated with the aerobic endurance indices obtained from incremental test (r > 0.70). These variables showed adequate sensitivity index (> 1). TT5km is a valid test to rank the aerobic endurance fitness of well-trained cyclists and to differentiate changes on aerobic endurance performance. Coaches can detect performance changes through either absolute (± 17.7 W) or relative power output (± 0.3 W.kg(-1)), the time to complete the test (± 13.4 s) and the average speed (± 1.0 km.h(-1)). Furthermore, TT5km performance can also be used to rank the athletes according to their aerobic endurance fitness.

  16. The glucagon test in the diagnosis of growth hormone deficiency in children with short stature younger than 6 years.

    Science.gov (United States)

    Secco, Andrea; di Iorgi, Natascia; Napoli, Flavia; Calandra, Erika; Ghezzi, Michele; Frassinetti, Costanza; Parodi, Stefano; Casini, Maria Rosaria; Lorini, Renata; Loche, Sandro; Maghnie, Mohamad

    2009-11-01

    Few studies have addressed the diagnostic role of the glucagon test in children with suspected GH deficiency (GHD). The objective of the study was to investigate the diagnostic value of the glucagon test as an alternative test to insulin tolerance test (ITT) and arginine in GHD children younger than 6 yr. This study was conducted in two pediatric endocrinology centers. Forty-eight children (median age 4.2 yr, median height -3.0 sd score) with GHD confirmed by a peak GH to ITT and arginine less than 10 microg/liter (median 4.7 and 3.4 microg/liter, respectively) underwent a glucagon stimulation test. Magnetic resonance imaging showed normal hypothalamic-pituitary anatomy in 24 children, isolated anterior pituitary hypoplasia in seven, and structural hypothalamic-pituitary abnormalities in 17. Median GH peak response to glucagon (13.5 microg/liter) was significantly higher than that observed after ITT and arginine (P short stature. Normative data for this test in young children need to be established before its use in clinical practice.

  17. Definition of the applicability domain of the Short Time Exposure (STE) test for predicting the eye irritation of chemicals.

    Science.gov (United States)

    Hayashi, Kazuhiko; Abo, Takayuki; Nukada, Yuko; Sakaguchi, Hitoshi

    2013-05-01

    The Short Time Exposure (STE) test is a simple and easy-to-perform in vitro eye irritation test, that uses the viability of SIRC cells (a rabbit corneal cell line) treated for five minutes as the endpoint. In this study, our goal was to define the applicability domain of the STE test, based on the results obtained with a set of 113 substances. To achieve this goal, chemicals were selected to represent both different chemical classes and different chemical properties, as well as to cover, in a balanced manner, the categories of eye irritation potential according to the Globally Harmonised System (GHS). Accuracy analysis indicated that the rates of false negatives for organic/inorganic salts (75.0%), hydrocarbons (33.3%) and alcohols (23.5%) were high. Many of the false negative results were for solid substances. It is noteworthy that no surfactant resulted in a false negative result in the STE test. Further examination of the physical property data and performance showed a significant improvement in the predictive accuracy, when substances with vapour pressures over 6kPa were excluded from the analyses. Our results indicate that several substances - i.e. certain solids such as salts, alcohols, hydrocarbons, and volatile substances with a vapour pressure over 6kPa - do not fall within the applicability domain of the STE test. Overall, we are encouraged by the performance and improved accuracy of the STE test. 2013 FRAME.

  18. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

    Directory of Open Access Journals (Sweden)

    Luisa W. Hugerth

    2017-09-01

    Full Text Available Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

  19. Allelic Tests and Sequence Analysis of Three Genes for Resistance to Xanthomonas perforans Race T3 in Tomato

    Institute of Scientific and Technical Information of China (English)

    ZHAO Baimei; CAO Haipeng; DUAN Junjie; YANG Wencai

    2015-01-01

    Three crosses,Hawaii7981×PI128216,Hawaii7981×LA1589,and PI128216×LA1589,were made to develop F2 populations for testing allelism among three genes Xv3,Rx4,and RxLA1589 conferring resistance to bacterial spot caused by Xanthomonas perforans race T3 in tomato. Each population consisted of 535–1 655 individuals. An infiltration method was used to inoculate the leaves of the parental and F2 plants as well as the susceptible control OH88119 for detecting hypersensitive resistance(HR). The results showed that all the tomato plants except OH88119 had HR to race T3,indicating that Xv3,Rx4,and RxLA1589 were allelic genes. Genomic DNA fragments of the Rx4 alleles from Hawaii7981,PI128216,and LA1589 were amplified using gene-specific primers and sequenced. No sequence variation was observed in the coding region of Rx4 in the three resistant lines. Based on the published map positions of these loci as well as the allelic tests and sequence data obtained in this study,we speculated that Xv3,Rx4,and RxLA1589 were the same gene. The results will provide useful information for understanding the mechanism of resistance to race T3 and developing resistant tomato varieties.

  20. Testing Scaling Relations for Solar-like Oscillations from the Main Sequence to Red Giants Using Kepler Data

    DEFF Research Database (Denmark)

    Huber, D.; Bedding, T.R.; Stello, D.

    2011-01-01

    ), and oscillation amplitudes. We show that the difference of the Δν-νmax relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M) s......We have analyzed solar-like oscillations in ~1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power (νmax), the large frequency separation (Δν...... scaling nor the revised scaling relation by Kjeldsen & Bedding is accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main sequence to red giants to a precision of ~25%. The residuals show...

  1. Description of the PMAD DC test bed architecture and integration sequence

    Science.gov (United States)

    Beach, R. F.; Trash, L.; Fong, D.; Bolerjack, B.

    1991-01-01

    NASA-LEWIS is responsible for the development, fabrication, and assembly of the electric power system (EPS) for the Space Station Freedom (SSF). The SSF power system is radically different from previous spacecraft power systems in both the size and complexity of the system. Unlike past spacecraft power systems, the SSF EPS will grow and be maintained on orbit and must be flexible to meet challenging user power needs. The SSF power system is also unique in comparison with terrestrial power systems because it is dominated by power electronic converters which regulate and control the power. A description is provided of the Power Management and Distribution DC Testbed which was assembled to support the design and early evaluation of the SSF EPS. A description of the integration process used in the assembly sequence is also given along with a description of the support facility.

  2. Retrospective Evaluations of Sequences: Testing the Predictions of a Memory-Based Analysis.

    Science.gov (United States)

    Aldrovandi, Silvio; Poirier, Marie; Kusev, Petko; Ayton, Peter

    2015-01-01

    Retrospective evaluation (RE) of event sequences is known to be biased in various ways. The present paper presents a series of studies that examined the suggestion that the moments that are the most accessible in memory at the point of RE contribute to these biases. As predicted by this memory-based analysis, Experiment 1 showed that pleasantness ratings of word lists were biased by the presentation position of a negative item and by how easy the negative information was to retrieve. Experiment 2 ruled out the hypothesis that these findings were due to the dual nature of the task called upon. Experiment 3 further manipulated the memorability of the negative items--and corresponding changes in RE were as predicted. Finally, Experiment 4 extended the findings to more complex stimuli involving event narratives. Overall, the results suggest that assessments were adjusted based on the retrieval of the most readily available information.

  3. Short Communication Phylogenetic Characterization of HIV Type 1 CRF01_AE V3 Envelope Sequences in Pregnant Women in Northern Vietnam

    Science.gov (United States)

    Caridha, Rozina; Ha, Tran Thi Thanh; Gaseitsiwe, Simani; Hung, Pham Viet; Anh, Nguyen Mai; Bao, Nguyen Huy; Khang, Dinh Duy; Hien, Nguyen Tran; Cam, Phung Dac; Chiodi, Francesca

    2012-01-01

    Abstract Characterization of HIV-1 strains is important for surveillance of the HIV-1 epidemic. In Vietnam HIV-1-infected pregnant women often fail to receive the care they are entitled to. Here, we analyzed phylogenetically HIV-1 env sequences from 37 HIV-1-infected pregnant women from Ha Noi (n=22) and Hai Phong (n=15), where they delivered in 2005–2007. All carried CRF01_AE in the gp120 V3 region. In 21 women CRF01_AE was also found in the reverse transcriptase gene. We compared their env gp120 V3 sequences phylogenetically in a maximum likelihood tree to those of 198 other CRF01_AE sequences in Vietnam and 229 from neighboring countries, predominantly Thailand, from the HIV-1 database. Altogether 464 sequences were analyzed. All but one of the maternal sequences colocalized with sequences from northern Vietnam. The maternal sequences had evolved the least when compared to sequences collected in Ha Noi in 2002, as shown by analysis of synonymous and nonsynonymous changes, than to other Vietnamese sequences collected earlier and/or elsewhere. Since the HIV-1 epidemic in women in Vietnam may still be underestimated, characterization of HIV-1 in pregnant women is important to observe how HIV-1 has evolved and follow its molecular epidemiology. PMID:21936713

  4. Relationship between physiological indices and aerobic performance tests in short and medium term of elite cyclists

    Directory of Open Access Journals (Sweden)

    Eduardo Bernardo Sangali

    2013-05-01

    Full Text Available Few studies allow usto verify which physiological responses are associated with performance in anational elite cycling group. Therefore, this study aimed to determine and correlate various physiological and aerobic indices with performance in 4 and 20 km time trials in high-level cyclists. The sample consisted of 14 male professional cyclists of the national elite group (28.5 ± 4.7 years old, 73.47 ± 8.29 kg, 176 ± 6.76cm, who performed a progressive test in laboratory to determine maximal oxygen consumption (VO2max: 62.23 ± 8.28 ml•kg-1•min-1, intensity relative to VO2max(iVO2max: 500.83 ± 58.65w, movement economy (EM: 0.1166 ± 0.0362 ml•kg•min•w-1, and the first and second ventilatory threshold (LV1: 348.21 ±43.26 w; LV2: 417.86 ± 60.79 w, respectively. They also performed two time trial performance tests of 4 and 20km. For the correlation between physiological indices and trial performance, Pearson correlation coefficient(p< 0.05 was used. No correlation was found between the physiological indices (VO2max absolute and relative, iVO2max, EM, LV1 and LV2 andperformance in 4 km (r= 0.38; 0.16; -0.33; 0.20; -0.50; -0.20, respectivelyand 20 km (r= 0.24; 0.01; -0.13; -0.12; -0.48; -0.19, respectively time trialin high level athletes. These results suggest that these variables are not able to explain the performance in time trials in the respective lengths, probably due to the subjects’ homogeneity.

  5. Distribution of Campylobacter jejuni isolates from turkey farms and different stages at slaughter using pulsed-field gel electrophoresis and flaA-short variable region sequencing.

    Science.gov (United States)

    Perko-Mäkelä, P; Alter, T; Isohanni, P; Zimmermann, S; Lyhs, U

    2011-09-01

    The aim of this study was to assess the diversity of thermotolerant Campylobacter spp. isolated from turkey flocks at six rearing farms 1-2 weeks prior to slaughter (360 faecal swab samples) and from 11 different stages at the slaughterhouse (636 caecal, environmental, neck skin and meat samples). A total of 121 Campylobacter isolates were identified to species level using a multiplex PCR assay and were typed by pulsed-field gel electrophoresis (PFGE) and flaA-short variable region (SVR) sequencing. All Campylobacter isolates were identified as Campylobacter jejuni. PFGE analysis with KpnI restriction enzyme resulted in 11 PFGE types (I-XI) and flaA SVR typing yielded in nine flaA-SVR alleles. The Campylobacter-positive turkey flocks A, C and E were colonized by a limited number of Campylobacter clones at the farm and slaughter. The present study confirms the traceability of flock-specific strains (PFGE types I, V and IX; flaA types 21, 36 and 161) from the farm along the entire processing line to meat cuts. It seems that stress factors such as high temperature of the defeathering water (54-56 °C), drying of the carcass skin during air chilling (24 h at 2 °C), and oxygen in the air could not eliminate Campylobacter completely. Campylobacter-negative flocks became contaminated during processing by the same subtypes of Campylobacter introduced into the slaughter house by preceeding positive flocks even if they were slaughtered on subsequent days. Proper and efficient cleaning and disinfection of slaughter and processing premises are needed to avoid cross-contamination, especially in countries with a low prevalence of Campylobacter spp. The majority of flaA SVR alleles displayed a distinct association with a specific PFGE type. However, a linear relationship for all strains among both typing methods could not be established. To specify genetic relatedness of strains, a combination of different genotyping methods, is needed. © 2011 Blackwell Verlag GmbH.

  6. tscvh R Package: Computational of the two samples test on microarray-sequencing data

    Science.gov (United States)

    Fajriyah, Rohmatul; Rosadi, Dedi

    2017-12-01

    We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

  7. Test of Lorentz and CPT violation with short baseline neutrino oscillation excesses

    Energy Technology Data Exchange (ETDEWEB)

    Aguilar-Arevalo, A.A. [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, D.F. 04510 (Mexico); Anderson, C.E. [Yale University, New Haven, CT 06520 (United States); Bazarko, A.O. [Princeton University, Princeton, NJ 08544 (United States); Brice, S.J.; Brown, B.C. [Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Bugel, L. [Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Cao, J. [University of Michigan, Ann Arbor, MI 48109 (United States); Coney, L. [Columbia University, New York, NY 10027 (United States); Conrad, J.M. [Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Cox, D.C. [Indiana University, Bloomington, IN 47405 (United States); Curioni, A. [Yale University, New Haven, CT 06520 (United States); Dharmapalan, R. [University of Alabama, Tuscaloosa, AL 35487 (United States); Djurcic, Z. [Argonne National Laboratory, Argonne, IL 60439 (United States); Finley, D.A. [Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Fleming, B.T. [Yale University, New Haven, CT 06520 (United States); Ford, R.; Garcia, F.G. [Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Garvey, G.T. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Grange, J. [University of Florida, Gainesville, FL 32611 (United States); Green, C. [Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); and others

    2013-01-29

    The sidereal time dependence of MiniBooNE {nu}{sub e} and {nu}{sup Macron }{sub e} appearance data is analyzed to search for evidence of Lorentz and CPT violation. An unbinned Kolmogorov-Smirnov (K-S) test shows both the {nu}{sub e} and {nu}{sup Macron }{sub e} appearance data are compatible with the null sidereal variation hypothesis to more than 5%. Using an unbinned likelihood fit with a Lorentz-violating oscillation model derived from the Standard Model Extension (SME) to describe any excess events over background, we find that the {nu}{sub e} appearance data prefer a sidereal time-independent solution, and the {nu}{sup Macron }{sub e} appearance data slightly prefer a sidereal time-dependent solution. Limits of order 10{sup -20} GeV are placed on combinations of SME coefficients. These limits give the best limits on certain SME coefficients for {nu}{sub {mu}}{yields}{nu}{sub e} and {nu}{sup Macron }{sub {mu}}{yields}{nu}{sup Macron }{sub e} oscillations. The fit values and limits of combinations of SME coefficients are provided.

  8. Short-term forecasting of non-OPEC supply: a test of seasonality and seasonal decomposition

    International Nuclear Information System (INIS)

    Jazayeri, S.M.R.T.; Yahyai, A.

    2002-01-01

    The purpose of this study is, first to find out, based on historical data, whether quarterly averages of non-OPEC supply follow a seasonal pattern. If that is mathematically established, then, secondly, it is attempted to estimate the best seasonal factors to decompose the estimated yearly average into seasonal averages. This study applies the Fourier analysis to quarterly supply series to test for seasonality, and provides estimates of seasonal factors for the year 2001 by applying the so-called X-11 decomposition method to the annual estimate. A set of historical data, consisting of quarterly supply averages of individual countries, regional subtotals and aggregate non-OPEC for the period 1971-2000, forms the basis of the analysis. Through the application of the Fourier analysis and X-11 decomposition method, it is demonstrated that quarterly non-OPEC supply, be it by an individual major producer or regional sub-totals, clearly follows a seasonal pattern. This is a very useful conclusion for the market analyst involved with forecasting the quarterly supply. (author)

  9. Short-term effect of dark chocolate consumption on routine haemostasis testing.

    Science.gov (United States)

    Montagnana, Martina; Danese, Elisa; Salvagno, Gian Luca; Lippi, Giuseppe

    2017-08-01

    This experimental study was designed to investigate the sort-term impact of dark chocolate ingestion on routine haemostasis tests in healthy volunteers. The study population consisted in 15 healthy male volunteers who ingested 50 g of 90% cocoa chocolate within 3-5 min. Blood was drawn early in the morning, immediately before chocolate ingestion and 4 h afterwards, for assessment of activated partial thromboplastin time (APTT), prothrombin time (PT) and fibrinogen. A significant increase of triglycerides (1.4 ± 0.6 versus 1.0 ± 0.5 mmol/L; p < .001), APTT (32.1 ± 2.2 versus 31.1 ± 2.0 s; p < .001) and PT (9.8 ± 0.5 versus 9.7 ± 0.4 s; p = .008) was observed 4 h after ingestion of dark chocolate, whereas fibrinogen values remained unchanged (2.6 ± 0.5 versus 2.5 ± 0.5 g/L; p = .063). Overall, we observed a mean percentage increase of 3.1% for APTT and 1.2% for PT. These results suggest that dark chocolate intake may have an impact on secondary haemostasis.

  10. Test of Lorentz and CPT violation with short baseline neutrino oscillation excesses

    International Nuclear Information System (INIS)

    Aguilar-Arevalo, A.A.; Anderson, C.E.; Bazarko, A.O.; Brice, S.J.; Brown, B.C.; Bugel, L.; Cao, J.; Coney, L.; Conrad, J.M.; Cox, D.C.; Curioni, A.; Dharmapalan, R.; Djurcic, Z.; Finley, D.A.; Fleming, B.T.; Ford, R.; Garcia, F.G.; Garvey, G.T.; Grange, J.; Green, C.

    2013-01-01

    The sidereal time dependence of MiniBooNE ν e and ν ¯ e appearance data is analyzed to search for evidence of Lorentz and CPT violation. An unbinned Kolmogorov–Smirnov (K–S) test shows both the ν e and ν ¯ e appearance data are compatible with the null sidereal variation hypothesis to more than 5%. Using an unbinned likelihood fit with a Lorentz-violating oscillation model derived from the Standard Model Extension (SME) to describe any excess events over background, we find that the ν e appearance data prefer a sidereal time-independent solution, and the ν ¯ e appearance data slightly prefer a sidereal time-dependent solution. Limits of order 10 −20 GeV are placed on combinations of SME coefficients. These limits give the best limits on certain SME coefficients for ν μ →ν e and ν ¯ μ →ν ¯ e oscillations. The fit values and limits of combinations of SME coefficients are provided.

  11. Role of serial order in the impact of talker variability on short-term memory: testing a perceptual organization-based account.

    Science.gov (United States)

    Hughes, Robert W; Marsh, John E; Jones, Dylan M

    2011-11-01

    In two experiments, we examined the impact of the degree of match between sequential auditory perceptual organization processes and the demands of a short-term memory task (memory for order vs. item information). When a spoken sequence of digits was presented so as to promote its perceptual partitioning into two distinct streams by conveying it in alternating female (F) and male (M) voices (FMFMFMFM)--thereby disturbing the perception of true temporal order--recall of item order was greatly impaired (as compared to recall of item identity). Moreover, an order error type consistent with the formation of voice-based streams was committed more quickly in the alternating-voice condition (Exp. 1). In contrast, when the perceptual organization of the sequence mapped well onto an optimal two-group serial rehearsal strategy--by presenting the two voices in discrete clusters (FFFFMMMM)--order, but not item, recall was enhanced (Exp. 2). The results are consistent with the view that the degree of compatibility between perceptual and deliberate sequencing processes is a key determinant of serial short-term memory performance. Alternative accounts of talker variability effects in short-term memory, based on the concept of a dedicated phonological short-term store and a capacity-limited focus of attention, are also reviewed.

  12. Psychometric test of the Team Climate Inventory-short version investigated in Dutch quality improvement teams

    Directory of Open Access Journals (Sweden)

    Nieboer Anna P

    2009-07-01

    Full Text Available Abstract Background Although some studies have used the Team Climate Inventory within teams working in health care settings, none of these included quality improvement teams. The aim of our study is to investigate the psychometric properties of the 14-item version of the Team Climate Inventory in healthcare quality improvement teams participating in a Dutch quality collaborative. Methods This study included quality improvement teams participating in the Care for Better improvement program for home care, care for the handicapped and the elderly in the Netherlands between 2006 and 2008. As part of a larger evaluation study 270 written questionnaires from team members were collected at baseline and 139 questionnaires at end measurement. Confirmatory factor analyses, reliability, Pearson correlations and paired samples t-tests were conducted to investigate construct validity, reliability, predictive validity and temporal stability. Results Confirmatory factor analyses revealed the expected four-factor structure and good fit indices. For the four subscales – vision, participative safety, task orientation and support for innovation – acceptable Cronbach's alpha coefficients and high inter-item correlations were found. The four subscales all proved significant predictors of perceived team effectiveness, with participatory safety being the best predictor. As expected the four subscales were found to be stable over time; i.e. without significant changes between baseline and end measurement. Conclusion The psychometric properties of the Dutch version of the TCI-14 are satisfactory. Together these results show that the TCI-14 is a useful instrument to assess to what extent aspects of team climate influence perceived team effectiveness of quality improvement teams.

  13. Psychometric test of the Team Climate Inventory-short version investigated in Dutch quality improvement teams.

    Science.gov (United States)

    Strating, Mathilde M H; Nieboer, Anna P

    2009-07-24

    Although some studies have used the Team Climate Inventory within teams working in health care settings, none of these included quality improvement teams. The aim of our study is to investigate the psychometric properties of the 14-item version of the Team Climate Inventory in healthcare quality improvement teams participating in a Dutch quality collaborative. This study included quality improvement teams participating in the Care for Better improvement program for home care, care for the handicapped and the elderly in the Netherlands between 2006 and 2008. As part of a larger evaluation study 270 written questionnaires from team members were collected at baseline and 139 questionnaires at end measurement. Confirmatory factor analyses, reliability, Pearson correlations and paired samples t-tests were conducted to investigate construct validity, reliability, predictive validity and temporal stability. Confirmatory factor analyses revealed the expected four-factor structure and good fit indices. For the four subscales--vision, participative safety, task orientation and support for innovation--acceptable Cronbach's alpha coefficients and high inter-item correlations were found. The four subscales all proved significant predictors of perceived team effectiveness, with participatory safety being the best predictor. As expected the four subscales were found to be stable over time; i.e. without significant changes between baseline and end measurement. The psychometric properties of the Dutch version of the TCI-14 are satisfactory. Together these results show that the TCI-14 is a useful instrument to assess to what extent aspects of team climate influence perceived team effectiveness of quality improvement teams.

  14. The congruency sequence effect 3.0: a critical test of conflict adaptation.

    Science.gov (United States)

    Duthoo, Wout; Abrahamse, Elger L; Braem, Senne; Boehler, C Nico; Notebaert, Wim

    2014-01-01

    Over the last two decades, the congruency sequence effect (CSE) -the finding of a reduced congruency effect following incongruent trials in conflict tasks- has played a central role in advancing research on cognitive control. According to the influential conflict-monitoring account, the CSE reflects adjustments in selective attention that enhance task focus when needed, often termed conflict adaptation. However, this dominant interpretation of the CSE has been called into question by several alternative accounts that stress the role of episodic memory processes: feature binding and (stimulus-response) contingency learning. To evaluate the notion of conflict adaptation in accounting for the CSE, we construed versions of three widely used experimental paradigms (the colour-word Stroop, picture-word Stroop and flanker task) that effectively control for feature binding and contingency learning. Results revealed that a CSE can emerge in all three tasks. This strongly suggests a contribution of attentional control to the CSE and highlights the potential of these unprecedentedly clean paradigms for further examining cognitive control.

  15. The congruency sequence effect 3.0: a critical test of conflict adaptation.

    Directory of Open Access Journals (Sweden)

    Wout Duthoo

    Full Text Available Over the last two decades, the congruency sequence effect (CSE -the finding of a reduced congruency effect following incongruent trials in conflict tasks- has played a central role in advancing research on cognitive control. According to the influential conflict-monitoring account, the CSE reflects adjustments in selective attention that enhance task focus when needed, often termed conflict adaptation. However, this dominant interpretation of the CSE has been called into question by several alternative accounts that stress the role of episodic memory processes: feature binding and (stimulus-response contingency learning. To evaluate the notion of conflict adaptation in accounting for the CSE, we construed versions of three widely used experimental paradigms (the colour-word Stroop, picture-word Stroop and flanker task that effectively control for feature binding and contingency learning. Results revealed that a CSE can emerge in all three tasks. This strongly suggests a contribution of attentional control to the CSE and highlights the potential of these unprecedentedly clean paradigms for further examining cognitive control.

  16. Test procedures to detect a loss of material in a sequence of balance periods

    International Nuclear Information System (INIS)

    Avenhaus, R.; Beedgen, R.; Sellinschegg, D.

    1985-06-01

    A workshop on Near-Real-Time Accountancy (NRTA) was held in KfK which came to a preliminary end in December 1982. In the framework of this workshop a number of sequential statistical test procedures were proposed which can be used in the case of a NRTA based safeguards regime. In the report the most promising test procedures are investigated. The analysis is based on the chemical separation process of a large model reprocessing facility with a throughput or 1000 tonnes per year. (orig.) [de

  17. The short-circuit test results of 6.9 kV/2.3 kV 400 kVA-class YBCO model transformer

    International Nuclear Information System (INIS)

    Tomioka, A.; Otonari, T.; Ogata, T.; Iwakuma, M.; Okamoto, H.; Hayashi, H.; Iijima, Y.; Saito, T.; Gosho, Y.; Tanabe, K.; Izumi, T.; Shiohara, Y.

    2011-01-01

    The 6.9 kV/2.3 kV 400 kVA-class single-phase YBCO model transformer with the YBCO tape with copper tape was manufactured for short-circuit current test. Short-circuit test was performed and the short-circuit current of primary winding was 346 A which was about six times larger than the rated current. The I-V characteristics of the winding did not change before and after the test. The transformer withstood short-circuit current. We are planning to turn the result into a consideration of a 66 kV/6.9 kV-20 MVA-class three-phase superconducting transformer. We are developing an elemental technology for 66 kV/6.9 kV 20 MVA-class power transformer with YBCO conductors. The protection of short-circuit technology is one of the elemental technologies for HTS transformer. Since short-circuit current is much higher than critical current of YBCO tape, there is a possibility that superconducting characteristics may be damaged during short-circuit period. We made a conductor to compose the YBCO tape with copper tape. We manufactured 6.9 kV/2.3 kV 400 kVA-class YBCO model transformer using this conductor and performed short-circuit current test. The short-circuit current of primary winding was 346 A which was about six times larger than the rated current. The I-V characteristics of the winding did not change before and after the test. We may consider this conductor withstands short-circuit current.

  18. Omnibus test for change detection in a time sequence of polarimetric SAR data

    DEFF Research Database (Denmark)

    Nielsen, Allan Aasbjerg; Conradsen, Knut; Skriver, Henning

    2016-01-01

    in the covariance matrix representation is carried out. The omnibus test statistic and its factorization detect if and when change(s) occur. The technique is demonstrated on airborne EMISAR C-band data but may be applied to ALOS, COSMO-SkyMed, RadarSat-2, Sentinel-1, TerraSAR-X, and Yoagan or other dual- and quad...

  19. Study to Analyze the Acquisition of Automatic Test Equipment (ATE) Systems. Data Sequence Number A003

    Science.gov (United States)

    1973-12-27

    Systems Test Equipment Comparator, ASTEC ) at NAEC can provide a very accurate Ion a pin by pin basis) match between the UUT and ATE in their data bank...In addition, abbreviated summary data on the ATE is also available to users. ASTEC will also file the UUT data as part of its data bank so that

  20. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  1. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  2. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    Science.gov (United States)

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Kinematic Orbit Determination Method Optimization and Test Analysis for BDS Satellites with Short-arc Tracking Data

    Directory of Open Access Journals (Sweden)

    GUO Rui

    2017-04-01

    Full Text Available Rapid orbit recovery is a puzzle for the BDS satellites after orbit maneuvers. Two kinematic orbit determination methods are studied, with two orbit determination models being established. The receiver system error and serious multipath error exist in the BDS system. The co-location method is proposed to estimate and calibrate the receiver system errors. A CNMC (code noise and multipath correction method is introduced to weaken the multipath error. Therefore the data quality is controlled efficiently for the receivers in the short tracking arc. The GEO/IGSO/MEO real data is emploied to carry out tests and validation. Using 10 min short tracking arc, the kinematic precise orbit determination accuracy is about 3.27 m for the GEOs, and 8.19 m for the IGSOs, and 5.9 m for the MEOs. Rapid orbit determination is achieved, which satisfying the orbit requirements from the BDS RDSS services. The kinematic precise orbit determination method also supports the RDSS service walking up to the global world.

  4. Assembly Tests of the First Nb$_{3}$Sn Low-Beta Quadrupole Short Model for the Hi-Lumi LHC

    CERN Document Server

    Pan, H; Cheng, D W; Anderssen, E; Ambrosio, G; Perez, J C; Juchno, M; Ferracin, P; Prestemon, S O

    2016-01-01

    In preparation for the high-luminosity upgrade of the Large Hadron Collider (LHC), the LHC Accelerator Research Program (LARP) in collaboration with CERN is pursuing the development of MQXF: a 150-mm-aperture high-field Nb$_{3}$Sn quadrupole magnet. The development phase starts with the fabrication and test of several short models (1.2-m magnetic length) and will continue with the development of several long prototypes. All of them are mechanically supported using a shell-based support structure, which has been extensively demonstrated on several R&D; models within LARP. The first short model MQXFS-AT has been assembled at LBNL with coils fabricated by LARP and CERN. In this paper, we summarize the assembly process and show how it relies strongly on experience acquired during the LARP 120-mm-aperture HQ magnet series. We present comparison between strain gauges data and finite-element model analysis. Finally, we present the implication of the MQXFS-AT experience on the design of the long prototype support...

  5. Three dimensional sampling perfection with application-optimized contrasts by using different flip angle evolutions-short time of the inversion recovery sequence for the post-ganglionic segments of the brachial plexus

    International Nuclear Information System (INIS)

    Fu Naiqi; Zhou Hongyu; Zheng Zhuozhao; Zhao Qiang

    2013-01-01

    Objective: To evaluate the contrast-enhanced 3D sampling perfection with application-optimized contrasts by using different flip angle evolutions-short TI inversion recovery sequence (SPACE-STIR) for the imaging of the post-ganglionic segments of the brachial plexus. Methods: Forty-three patients with suspected brachial plexus lesions were examined with 3D SPACE-STIR and contrast-enhanced 3D SPACE-STIR prospectively. Signal-to-noise ratios (SNR), contrast-to-noise ratios (CNR), and the conspicuousness of roots, trunks,divisions and cords of the brachial plexus of the two 3D sequences were retrospectively compared. Statistical analysis was performed by using student t-test and Wilcoxon rank sum test. Results: Compared with 3D SPACE-STIR, contrast-enhanced 3D SPACE-STIR provided the similar SNRs (left, 37.41 ± 7.34 vs 36.27 ± 7.66, t = 1.574, P = 0.123, right, 43.85 ± 9.56 vs 42.34 ± 9.74, t = 1.937, P = 0.073), but significantly higher nerve-to-muscle CNRs (left, 24.01 ± 6.31 vs 26.39 ± 6.95, right, 29.31 ± 7.84 vs 31.77 ± 8.85, t = -3.278, -3.278, both P < 0.01) and nerve-to-lymph gland CNRs(left, -0.84 ± 10.51 vs 15.35 ± 8.02, right, -8.47 ± 10.85 vs 19.30 ± 10.35, t = -15.984, -15.651, both P < 0.01). The conspicuousness of roots and trunks on contrast-enhanced 3D SPACE-STIR was significantly better than that on 3D SPACE-STIR (Z = -3.606, -4.472, P < 0.01), while the conspicuousness of divisions and cords was similar(Z = -1.732, -1.414, P = 0.083, 0.157). The signal intensity of neoplastic lesions on contrast-enhanced 3D SPACE-STIR tended to decrease rapidly, thus the lesion conspicuousness was worse than that on 3D SPACE-STIR. Conclusions: Contrast-enhanced 3D SPACE-STIR has obvious advantages in displaying normal brachial plexus and revealing non-neoplastic lesions of the brachial plexus, but may be insufficient for the diagnosis of neoplastic lesions of the brachial plexus. (authors)

  6. Sequence and expression pattern of a novel human orphan G-protein-coupled receptor, GPRC5B, a family C receptor with a short amino-terminal domain

    DEFF Research Database (Denmark)

    Bräuner-Osborne, Hans; Krogsgaard-Larsen, P

    2000-01-01

    Query of GenBank with the amino acid sequence of human metabotropic glutamate receptor subtype 2 (mGluR2) identified a predicted gene product of unknown function on BAC clone CIT987SK-A-69G12 (located on chromosome band 16p12) as a homologous protein. The transcript, entitled GPRC5B, was cloned f...... from an expressed sequence tag clone that contained the entire open reading frame of the transcript encoding a protein of 395 amino acids. Analysis of the protein sequence reveal that GPRC5B contains a signal peptide and seven transmembrane alpha-helices, which is a hallmark of G...

  7. The University of Minnesota aquifer thermal energy storage (ATES) field test facility -- system description, aquifer characterization, and results of short-term test cycles

    Energy Technology Data Exchange (ETDEWEB)

    Walton, M.; Hoyer, M.C.; Eisenreich, S.J.; Holm, N.L.; Holm, T.R.; Kanivetsky, R.; Jirsa, M.A.; Lee, H.C.; Lauer, J.L.; Miller, R.T.; Norton, J.L.; Runke, H. (Minnesota Geological Survey, St. Paul, MN (United States))

    1991-06-01

    Phase 1 of the Aquifer Thermal Energy Storage (ATES) Project at the University of Minnesota was to test the feasibility, and model, the ATES concept at temperatures above 100{degrees}C using a confined aquifer for the storage and recovery of hot water. Phase 1 included design, construction, and operation of a 5-MW thermal input/output field test facility (FTF) for four short-term ATES cycles (8 days each of heat injection, storage, and heat recover). Phase 1 was conducted from May 1980 to December 1983. This report describes the FTF, the Franconia-Ironton-Galesville (FIG) aquifer used for the test, and the four short-term ATES cycles. Heat recovery; operational experience; and thermal, chemical, hydrologic, and geologic effects are all included. The FTF consists of monitoring wells and the source and storage well doublet completed in the FIG aquifer with heat exchangers and a fixed-bed precipitator between the wells of the doublet. The FIG aquifer is highly layered and a really anisotropic. The upper Franconia and Ironton-Galesville parts of the aquifer, those parts screened, have hydraulic conductivities of {approximately}0.6 and {approximately}1.0 m/d, respectively. Primary ions in the ambient ground water are calcium and magnesium bicarbonate. Ambient temperature FIG ground water is saturated with respect to calcium/magnesium bicarbonate. Heating the ground water caused most of the dissolved calcium to precipitate out as calcium carbonate in the heat exchanger and precipitator. Silica, calcium, and magnesium were significantly higher in recovered water than in injected water, suggesting dissolution of some constituents of the aquifer during the cycles. Further work on the ground water chemistry is required to understand water-rock interactions.

  8. Next generation sequencing for preimplantation genetic testing of blastocysts aneuploidies in women of different ages

    Directory of Open Access Journals (Sweden)

    Krzysztof Lukaszuk

    2015-12-01

    Full Text Available Most of the current preimplantation genetic screening of aneuploidies tests are based on the low quality and low density comparative genomic hybridization arrays. The results are based on fewer than 2,700 probes. Our main outcome was the association of aneuploidy rates and the women’s age. Between August–December 2013, 198 blastocysts from women (mean age 36.3+-4.6 undergoing in vitro fertilization underwent routine trophectoderm biopsy. NGS was performed on Ion Torrent PGM (Life Technologies. The results were analyzed in five age groups ( 40. 85 blastocysts were normal according to NGS results. The results in the investigated groups were (% of normal blastocyst in each group: 40 (38.5%. Our study suggests that NGS PGD is applicable for routine preimplantation genetic testing. It allows also for easy customization of the procedure for each individual patient making personalized diagnostics a reality.

  9. The Applicability of a Short-term Test for Detection of Modifying Effects of Dietary Factors in Rodent Colon Carcinogenesis

    DEFF Research Database (Denmark)

    Kristiansen, Eva

    The present studies were initiated to develop a short-term rodent model to assess the influence of different dietary components on the development of colon cancer. Diets with different dietary components, i.e. dietary fibre, fat, sucrose, and starches were tested in male rats initiated with DMH-2......HCl or AOM for their modulating effect on the development of aberrant crypt foci (ACF). Furthermore the heterocyclic amines IQ and PhIP were introduced in the assay as inducers of ACF in mice and rats and their role in colon carcinogenesis in mice was investigated. ACF were found to be induced...... in rodent colon by the colon carcinogens DMH-2HC1, AOM, IQ, and PhIP and it was shown that the incidence of the induced ACF could be modulated by dietary components such as sucrose, dietary fibre, and starch....

  10. Quick screening of cognitive function in Indian multiple sclerosis patients using Montreal cognitive assessment test-short version

    Directory of Open Access Journals (Sweden)

    Darshpreet Kaur

    2013-01-01

    Full Text Available Background: Cognitive impairments in multiple sclerosis (MS are now well recognized worldwide, but unfortunately this domain has been less explored in India due to many undermining factors. The aim of this study was to evaluate cognitive impairments in Indian MS patients with visual or upper limb motor problems with the help of short version of Montreal cognitive assessment test (MoCA. Subjects and Methods: Thirty MS patients and 50 matched controls were recruited for the 12 points MoCA task. Receiver operating characteristic curve (ROC analysis was performed to determine optimal sensitivity and specificity of the 12 points MoCA in differentiating cognitively impaired patients and controls. Results: The mean 12 points MoCA scores of the controls and MS patients were 11.56 ± 0.67 and 8.06 ± 1.99, respectively. In our study, the optimal cut-off value for 12 points MoCA to be able to differentiate patients with cognitive impairments from controls is 10/12. Accordingly, 73.3% patients fell below the cut off value. Both the groups did not have significant statistical differences with regard to age and educational years. Conclusion: The 12 points, short version of MoCA, is a useful brief screening tool for quick and early detection of mild cognitive impairments in subjects with MS. It can be administered to patients having visual and motor problems. It is of potential use by primary care physicians, nurses, and other allied health professionals who need a quick screening test. No formal training for administration is required. Financial and time constraints should not limit the use of the proposed instrument.

  11. TESTING SCALING RELATIONS FOR SOLAR-LIKE OSCILLATIONS FROM THE MAIN SEQUENCE TO RED GIANTS USING KEPLER DATA

    Energy Technology Data Exchange (ETDEWEB)

    Huber, D.; Bedding, T. R.; Stello, D. [Sydney Institute for Astronomy (SIfA), School of Physics, University of Sydney, NSW 2006 (Australia); Hekker, S. [Astronomical Institute ' Anton Pannekoek' , University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Mathur, S. [High Altitude Observatory, NCAR, P.O. Box 3000, Boulder, CO 80307 (United States); Mosser, B. [LESIA, CNRS, Universite Pierre et Marie Curie, Universite Denis, Diderot, Observatoire de Paris, 92195 Meudon cedex (France); Verner, G. A.; Elsworth, Y. P.; Hale, S. J.; Chaplin, W. J. [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Bonanno, A. [INAF Osservatorio Astrofisico di Catania (Italy); Buzasi, D. L. [Eureka Scientific, 2452 Delmer Street Suite 100, Oakland, CA 94602-3017 (United States); Campante, T. L. [Centro de Astrofisica da Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Kallinger, T. [Department of Physics and Astronomy, University of British Columbia, Vancouver (Canada); Silva Aguirre, V. [Max-Planck-Institut fuer Astrophysik, Karl-Schwarzschild-Str. 1, 85748 Garching (Germany); De Ridder, J. [Instituut voor Sterrenkunde, K.U.Leuven (Belgium); Garcia, R. A. [Laboratoire AIM, CEA/DSM-CNRS, Universite Paris 7 Diderot, IRFU/SAp, Centre de Saclay, 91191, Gif-sur-Yvette (France); Appourchaux, T. [Institut d' Astrophysique Spatiale, UMR 8617, Universite Paris Sud, 91405 Orsay Cedex (France); Frandsen, S. [Danish AsteroSeismology Centre (DASC), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C (Denmark); Houdek, G., E-mail: dhuber@physics.usyd.edu.au [Institute of Astronomy, University of Vienna, 1180 Vienna (Austria); and others

    2011-12-20

    We have analyzed solar-like oscillations in {approx}1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power ({nu}{sub max}), the large frequency separation ({Delta}{nu}), and oscillation amplitudes. We show that the difference of the {Delta}{nu}-{nu}{sub max} relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M){sup s} scaling nor the revised scaling relation by Kjeldsen and Bedding is accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main sequence to red giants to a precision of {approx}25%. The residuals show an offset particularly for unevolved stars, suggesting that an additional physical dependency is necessary to fully reproduce the observed amplitudes. We investigate correlations between amplitudes and stellar activity, and find evidence that the effect of amplitude suppression is most pronounced for subgiant stars. Finally, we test the location of the cool edge of the instability strip in the Hertzsprung-Russell diagram using solar-like oscillations and find the detections in the hottest stars compatible with a domain of hybrid stochastically excited and opacity driven pulsation.

  12. Empirical tests of pre-main-sequence stellar evolution models with eclipsing binaries

    Science.gov (United States)

    Stassun, Keivan G.; Feiden, Gregory A.; Torres, Guillermo

    2014-06-01

    We examine the performance of standard pre-main-sequence (PMS) stellar evolution models against the accurately measured properties of a benchmark sample of 26 PMS stars in 13 eclipsing binary (EB) systems having masses 0.04-4.0 M⊙ and nominal ages ≈1-20 Myr. We provide a definitive compilation of all fundamental properties for the EBs, with a careful and consistent reassessment of observational uncertainties. We also provide a definitive compilation of the various PMS model sets, including physical ingredients and limits of applicability. No set of model isochrones is able to successfully reproduce all of the measured properties of all of the EBs. In the H-R diagram, the masses inferred for the individual stars by the models are accurate to better than 10% at ≳1 M⊙, but below 1 M⊙ they are discrepant by 50-100%. Adjusting the observed radii and temperatures using empirical relations for the effects of magnetic activity helps to resolve the discrepancies in a few cases, but fails as a general solution. We find evidence that the failure of the models to match the data is linked to the triples in the EB sample; at least half of the EBs possess tertiary companions. Excluding the triples, the models reproduce the stellar masses to better than ∼10% in the H-R diagram, down to 0.5 M⊙, below which the current sample is fully contaminated by tertiaries. We consider several mechanisms by which a tertiary might cause changes in the EB properties and thus corrupt the agreement with stellar model predictions. We show that the energies of the tertiary orbits are comparable to that needed to potentially explain the scatter in the EB properties through injection of heat, perhaps involving tidal interaction. It seems from the evidence at hand that this mechanism, however it operates in detail, has more influence on the surface properties of the stars than on their internal structure, as the lithium abundances are broadly in good agreement with model predictions. The

  13. Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

    DEFF Research Database (Denmark)

    2017-01-01

    The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients...... with IS or LGS. The contribution of autosomal recessive genetic variation, however, is less well understood. We implemented a rare variant transmission disequilibrium test (TDT) to search for autosomal recessive epileptic encephalopathy genes in a cohort of 320 outbred patient-parent trios that were generally...... not find evidence of a role for individual autosomal recessive genes, our current sample is insufficiently powered to assess the overall role of autosomal recessive genotypes in an outbred epileptic encephalopathy population....

  14. Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region

    Directory of Open Access Journals (Sweden)

    Argüello-Astorga Gerardo R

    2010-10-01

    Full Text Available Abstract Background Euphorbia mosaic virus (EuMV is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep and virion-strand replication origin. The first entirely characterized EuMV isolate is native from Yucatan Peninsula, Mexico; subsequently, EuMV was detected in weeds and pepper plants from another region of Mexico, and partial DNA-A sequences revealed significant differences in their putative replication specificity determinants with respect to EuMV-YP. This study was aimed to investigate the replication compatibility between two EuMV isolates from the same country. Results A new isolate of EuMV was obtained from pepper plants collected at Jalisco, Mexico. Full-length clones of both genomic components of EuMV-Jal were biolistically inoculated into plants of three different species, which developed symptoms indistinguishable from those induced by EuMV-YP. Pseudorecombination experiments with EuMV-Jal and EuMV-YP genomic components demonstrated that these viruses do not form infectious reassortants in Nicotiana benthamiana, presumably because of Rep-iteron incompatibility. Sequence analysis of the EuMV-Jal DNA-B intergenic region (IR led to the unexpected discovery of a 35-nt-long sequence that is identical to a segment of the rep gene in the cognate viral DNA-A. Similar short rep sequences ranging from 35- to 51-nt in length were identified in all EuMV isolates and in three distinct viruses from South America related to EuMV. These short rep sequences in the DNA-B IR are positioned downstream to a ~160-nt non-coding domain highly similar to the CP promoter of begomoviruses belonging to the SLCV clade. Conclusions EuMV strains are not compatible in replication, indicating that this begomovirus species probably is not a replicating lineage in nature. The genomic analysis of EuMV-Jal led to the discovery of a subgroup of SLCV clade viruses that contain in

  15. Detecting dementia in patients with normal neuropsychological screening by Short Smell Test and Palmo-Mental Reflex Test: an observational study.

    Science.gov (United States)

    Streit, Sven; Limacher, Andreas; Zeller, Andreas; Bürge, Markus

    2015-07-25

    General practitioners (GPs) are in best position to suspect dementia. Mini-Mental State Examination (MMSE) and Clock Drawing Test (CDT) are widely used. Additional neurological tests may increase the accuracy of diagnosis. We aimed to evaluate diagnostic ability to detect dementia with a Short Smell Test (SST) and Palmo-Mental Reflex (PMR) in patients whose MMSE and CDT are normal, but who show signs of cognitive dysfunction. This was a 3.5-year cross-sectional observational study in the Memory Clinic of the University Department of Geriatrics in Bern, Switzerland. Participating patients with normal MMSE (>26 points) and CDT (>5 points) were referred by GPs because they suspected dementia. All were examined according to a standardized protocol. Diagnosis of dementia was based on DSM-IV TR criteria. We used SST and PMR to determine if they accurately detected dementia. In our cohort, 154 patients suspected of dementia had normal MMSE and CDT test results. Of these, 17 (11%) were demented. If SST or PMR were abnormal, sensitivity was 71% (95% CI 44-90%), and specificity 64% (95% CI 55-72%) for detecting dementia. If both tests were abnormal, sensitivity was 24% (95% CI 7-50%), but specificity increased to 93% (95% CI 88-97%). Patients suspected of dementia, but with normal MMSE and CDT results, may benefit if SST and PMR are added as diagnostic tools. If both SST and PMR are abnormal, this is a red flag to investigate these patients further, even though their negative neuropsychological screening results.

  16. Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing.

    Directory of Open Access Journals (Sweden)

    Matthew C Hiemenz

    Full Text Available Next-generation sequencing (NGS is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2. For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.

  17. Measuring Gratitude: A Comparative Validation of the Dutch Gratitude Questionnaire (GQ6 and Short Gratitude, Resentment, and Appreciation Test (SGRAT

    Directory of Open Access Journals (Sweden)

    Lilian Jans-Beken

    2015-05-01

    Full Text Available The aim of this article was to validate and compare the Dutch translations of the Gratitude Questionnaire (GQ6 and the Short Gratitude, Resentment, and Appreciation Test (SGRAT in an adult general population sample. In an online survey, 706 respondents ('M 'age = 44, 'SD 'age = 14 completed Dutch versions of the GQ6, the SGRAT, the Satisfaction With Life Scale (SWLS and the Positive Affect and Negative Affect Schedule (PANAS. At six week follow-up, 440 (62% of them ('M' age = 46, 'SD' age = 14 again completed the GQ6-NL and SGRAT-NL. Parallel analyses, exploratory factor analyses and confirmatory factor analyses revealed and confirmed one factor for the GQ6-NL, and three factors for the SGRAT-NL. Internal consistency indices of the GQ6-NL and of the SGRAT-NL were satisfactory. Both questionnaires demonstrated good test-retest reliability. Regression analyses showed, for the total scores on both gratitude questionnaires, positive associations with the SWLS and the Positive Affect Scale, and negative associations with the Negative Affect Scale. The results support the validity of the Dutch GQ6 and SGRAT. These questionnaires can be used to conduct further research of the grateful disposition in Dutch speaking individuals and groups.

  18. Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Isabella Bernardis

    2016-01-01

    Full Text Available To assess the clinical utility of targeted Next-Generation Sequencing (NGS for the diagnosis of Inherited Retinal Dystrophies (IRDs, a total of 109 subjects were enrolled in the study, including 88 IRD affected probands and 21 healthy relatives. Clinical diagnoses included Retinitis Pigmentosa (RP, Leber Congenital Amaurosis (LCA, Stargardt Disease (STGD, Best Macular Dystrophy (BMD, Usher Syndrome (USH, and other IRDs with undefined clinical diagnosis. Participants underwent a complete ophthalmologic examination followed by genetic counseling. A custom AmpliSeq™ panel of 72 IRD-related genes was designed for the analysis and tested using Ion semiconductor Next-Generation Sequencing (NGS. Potential disease-causing mutations were identified in 59.1% of probands, comprising mutations in 16 genes. The highest diagnostic yields were achieved for BMD, LCA, USH, and STGD patients, whereas RP confirmed its high genetic heterogeneity. Causative mutations were identified in 17.6% of probands with undefined diagnosis. Revision of the initial diagnosis was performed for 9.6% of genetically diagnosed patients. This study demonstrates that NGS represents a comprehensive cost-effective approach for IRDs molecular diagnosis. The identification of the genetic alterations underlying the phenotype enabled the clinicians to achieve a more accurate diagnosis. The results emphasize the importance of molecular diagnosis coupled with clinic information to unravel the extensive phenotypic heterogeneity of these diseases.

  19. Road and rail traffic noise induce comparable extra-aural effects as revealed during a short-term memory test

    Directory of Open Access Journals (Sweden)

    Eugen Gallasch

    2016-01-01

    Full Text Available To examine extraaural effects as induced by 20 min of road (ROAD and 20 min of rail (RAIL traffic noise with same loudness (75 dBA, a laboratory study was carried out. The study (N = 54 consisted of 28 high and 26 low-annoyed healthy individuals as determined by a traffic annoyance test. To control attention, all individuals performed a nonauditory short-term memory test during the noise exposures. A within-subject design, with phases of ROAD, RAIL, and CALM (memory test only, alternated by phases of rest, was defined. Heart rate (HR, systolic blood pressure (sBP, total peripheral resistance (TPR, as well as three autonomic variables, preejection period (PEP, 0.15–0.4 Hz high-frequency component of HR variability (HF, and salivary stress biomarker alpha amylase (sAA were measured. In relation to CALM, HR increased (RAIL +2.1%, ROAD +2.5%, sBP tended to increase against the end of noise exposure, PEP decreased (RAIL −0.7%, ROAD −0.8%, HF decreased (RAIL −3.4%, ROAD −2.9%, and sAA increased (RAIL +78%, ROAD +69%. No differences were found between RAIL and ROAD, indicating that both noise stressors induced comparable extraaural effects. Factor annoyance showed significant during CALM. Here a reduced sympathetic drive (higher PEP values combined with an increased vascular tone (higher TPR values was found at the high-annoyed subgroup.

  20. Proficiency Testing for Bacterial Whole Genome Sequencing: An End-User Survey of Current Capabilities, Requirements and Priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

    2015-01-01

    The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of ‘wet’ laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://​www.​globalmicrobiali​dentifier.​org/​) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted...... by Working Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range...

  1. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

    2015-01-01

    The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of 'wet' laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted by Working...... Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range of costs...

  2. Automated Scoring of Short-Answer Open-Ended GRE® Subject Test Items. ETS GRE® Board Research Report No. 04-02. ETS RR-08-20

    Science.gov (United States)

    Attali, Yigal; Powers, Don; Freedman, Marshall; Harrison, Marissa; Obetz, Susan

    2008-01-01

    This report describes the development, administration, and scoring of open-ended variants of GRE® Subject Test items in biology and psychology. These questions were administered in a Web-based experiment to registered examinees of the respective Subject Tests. The questions required a short answer of 1-3 sentences, and responses were automatically…

  3. Acceptability of, and Information Needs Regarding, Next-Generation Sequencing in People Tested for Hereditary Cancer: A Qualitative Study.

    Science.gov (United States)

    Meiser, Bettina; Storey, Ben; Quinn, Veronica; Rahman, Belinda; Andrews, Lesley

    2016-04-01

    Next generation sequencing (NGS) for patients at risk of hereditary cancer syndromes can also identify non-cancer related mutations, as well as variants of unknown significance. This study aimed to determine what benefits and shortcomings patients perceive in relation to NGS, as well as their interest and information preferences in regards to such testing. Eligible patients had previously received inconclusive results from clinical mutation testing for cancer susceptibility. Semi-structured telephone interviews were subjected to qualitative analysis guided by the approach developed by Miles and Huberman. The majority of the 19 participants reported they would be interested in panel/genomic testing. Advantages identified included that it would enable better preparation and allow implementation of individualized preventative strategies, with few disadvantages mentioned. Almost all participants said they would want all results, not just those related to their previous diagnosis. Participants felt that a face-to-face discussion supplemented by an information booklet would be the best way to convey information and achieve informed consent. All participants wanted their information stored and reviewed in accordance with new developments. Although the findings indicate strong interest among these individuals, it seems that the consent process, and the interpretation and communication of results will be areas that will require revision to meet the needs of patients.

  4. Development of a radionuclide short-test for the evaluation of engine oils in respect to cam- and cylinder linear wear by using OM 616 Kombi-Test conditions

    International Nuclear Information System (INIS)

    Volz, J.; Lausch, W.

    1980-05-01

    A survey is given on the studies performed since 1973 on the development of radionuclide short-test procedure, based on the test procedure of the OM 616 Kombi-Test, for the evaluation of engine oils in respect to cam- and cylinder liner wear (deuteron activated Co-56). Out of the results of these studies on experimental short test procedure has been elaborated to evaluate cylinder liner wear. With this experimental procedure some round robin testing has been carried out by three laboratories using a well-known reference oil and two test oils. The results of this round robin test led to further improvements in the test procedure. This improved test procedure has become a suitable screening-test for the development of engine oils in respect to cylinder liner wear. It never can replace the OM 616-Kombi-Test as a whole, but it will complete it. The radionuclide short test gets results quicker and at lower costs than the Kombi-Test, discriminates between hot test and cold-warm test results, and gives results even with correlation to the Kombi-Test by comparison to an approved reference oil. For such screening work, the repeatability of the test is also sufficient. (orig./HP) [de

  5. Internal consistency, reliability, and temporal stability of the Oxford Happiness Questionnaire short-form: Test-retest data over two weeks

    OpenAIRE

    MCGUCKIN, CONOR

    2006-01-01

    PUBLISHED The Oxford Happiness Questionnaire short-form is a recently developed eight-item measure of happiness. This study evaluated the internal consistency reliability and test-retest reliability of the Oxford Happiness Questionnaire short-form among 55 Northern Irish undergraduate university students who completed the measure on two occasions separated by two weeks. Internal consistency of the measure on both occasions was satisfactory at both Time 1 (alpha = .62) and Time 2 (alpha = ....

  6. Use of cardio-diagnostics of D&K-TEST for individualizations of training process of skilled short track speed skaters high qualification

    Directory of Open Access Journals (Sweden)

    Kygayevskiy S.A.

    2009-10-01

    Full Text Available In the article possibilities of individualization of training process of short track speed skaters high qualification are resulted on the basis of influence of application of loadings of different orientation on the indexes of cardio-diagnostics of D&K-TEST. The influences of loadings of different physiological and metabolic orientation given about efficiency are resulted on the level of functional preparedness of short track speed skaters of high qualification.

  7. Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida; Albrechtsen, Anders

    2013-01-01

    A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. Howeve......, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic regions....

  8. Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

    International Nuclear Information System (INIS)

    Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael; Hartmann, Arndt

    2017-01-01

    The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

  9. Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

    Energy Technology Data Exchange (ETDEWEB)

    Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael [Univ. Hospital Erlangen (Germany). Dept. of Radiology; Geppert, Christian [Siemens Healthcare GmbH, Erlangen (Germany); Hartmann, Arndt [Univ. Hospital Erlangen (Germany). Dept. of Pathology

    2017-02-15

    The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

  10. Sacubitril/valsartan and short-term changes in the 6-minute walk test: A pilot study.

    Science.gov (United States)

    Beltrán, Paola; Palau, Patricia; Domínguez, Eloy; Faraudo, Mercedes; Núñez, Eduardo; Guri, Olga; Mollar, Anna; Sanchis, Juan; Bayés-Genís, Antoni; Núñez, Julio

    2018-02-01

    Impaired exercise capacity is the most disabling symptom in patients with heart failure with reduced ejection fraction (HFrEF). Despite sacubitril/valsartan showing reduced long-term morbidity and mortality over enalapril in HFrEF, its effects on short-term functional capacity remain uncertain. We sought to evaluate the effects of sacubitril/valsartan on a 30-day six-minute walk test in eligible patients with HFrEF. From November 1, 2016 to February 1, 2017, a total of 58 stable symptomatic patients with HFrEF were eligible for sacubitril/valsartan and underwent 6-MWT before and 30days after initiation of sacubitril/valsartan therapy. A mixed-effects model for repeated-measures was used to analyze the changes. Mean age was 70±11years. 72.4% males, 46.6% with ischemic heart disease, and 51.7% on NYHA functional class III were included. The mean (SD) values of baseline LVEF and 6MWT were 30±7%, and 300±89m, respectively. The median (IQR) of NT-proBNP at baseline was 2701pg/ml (1087-4200). Compared with baseline, the 6-MWT distance increased significantly at 30days by 13.9% (+∆=41.8m (33.4-50.2); psacubitril/valsartan was associated with an improvement in exercise tolerance in symptomatic patients with HFrEF. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  11. Development and Short-Range Testing of a 100 kW Side-Illuminated Millimeter-Wave Thermal Rocket

    Science.gov (United States)

    Bruccoleri, Alexander; Eilers, James A.; Lambot, Thomas; Parkin, Kevin

    2015-01-01

    The objective of the phase described here of the Millimeter-Wave Thermal Launch System (MTLS) Project was to launch a small thermal rocket into the air using millimeter waves. The preliminary results of the first MTLS flight vehicle launches are presented in this work. The design and construction of a small thermal rocket with a planar ceramic heat exchanger mounted along the axis of the rocket is described. The heat exchanger was illuminated from the side by a millimeter-wave beam and fed propellant from above via a small tank containing high pressure argon or nitrogen. Short-range tests where the rocket was launched, tracked, and heated with the beam are described. The rockets were approximately 1.5 meters in length and 65 millimeters in diameter, with a liftoff mass of 1.8 kilograms. The rocket airframes were coated in aluminum and had a parachute recovery system activated via a timer and Pyrodex. At the rocket heat exchanger, the beam distance was 40 meters with a peak power intensity of 77 watts per square centimeter. and a total power of 32 kilowatts in a 30 centimeter diameter circle. An altitude of approximately 10 meters was achieved. Recommendations for improvements are discussed.

  12. Disentangling Gratitude: A Theoretical and Psychometric Examination of the Gratitude Resentment and Appreciation Test-Revised Short (GRAT-RS).

    Science.gov (United States)

    Hammer, Joseph H; Brenner, Rachel E

    2017-07-14

    This study extended our theoretical and applied understanding of gratitude through a psychometric examination of the most popular multidimensional measure of gratitude, the Gratitude, Resentment, and Appreciation Test-Revised Short form (GRAT-RS). Namely, the dimensionality of the GRAT-RS, the model-based reliability of the GRAT-RS total score and 3 subscale scores, and the incremental evidence of validity for its latent factors were assessed. Dimensionality measures (e.g., explained common variance) and confirmatory factor analysis results with 426 community adults indicated that the GRAT-RS conformed to a multidimensional (bifactor) structure. Model-based reliability measures (e.g., omega hierarchical) provided support for the future use of the Lack of a Sense of Deprivation raw subscale score, but not for the raw GRAT-RS total score, Simple Appreciation subscale score, or Appreciation of Others subscale score. Structural equation modeling results indicated that only the general gratitude factor and the lack of a sense of deprivation specific factor accounted for significant variance in life satisfaction, positive affect, and distress. These findings support the 3 pillars of gratitude conceptualization of gratitude over competing conceptualizations, the position that the specific forms of gratitude are theoretically distinct, and the argument that appreciation is distinct from the superordinate construct of gratitude.

  13. Short time evaluation of metallic materials' fatigue potential combining destructive and non-destructive testing methods

    International Nuclear Information System (INIS)

    Starke, Peter; Wu, Haoran; Boller, Christian

    2015-01-01

    Fatigue of engineering structures is an issue from an engineering design point. The lifetime of materials being subject to repeated mechanical loads is limited. Different examples of failures and fateful air accidents have caused significant cost and claims to the operators as well as manufacturers in excess of fatalities. Criticality of failure increases with increasing age and the uncertainty of operational loads applied. In such a case a reassessment of a structural materials' condition is in big need should damage tolerance criteria still be met, being the essential ground rule for aeronautical structural design. It is therefore the challenging aim to use a metallic material's microstructure characterizing non-destructive testing (NDT) parameter or a combination of those as a parameter to be scanned over a defined surface of the component considered to more realistically characterize the damage condition and to use this information twofold: (a) to more precisely assess the structural component's residual life and (b) to feed the information recorded back into a specific database belonging to an approach named PHYBAL. The physically based fatigue life evaluation method (PHYBAL) is a short-time procedure for the evaluation of fatigue data based on a small number of fatigue tests performed on un-notched specimens only. This method significantly reduces the effort for experimentation in terms of time and cost by around 90 % and inhibits remarkable scientific as well as economic advantages. The paper highlights the high capability of PHYBAL as well as the suitability for assessing the residual life of aeronautical components also with respect to the application of this approach in the light of structural health monitoring issues.

  14. Benign tracheobronchial stenoses: changes in short-term and long-term pulmonary function testing after expandable metallic stent placement.

    Science.gov (United States)

    Gotway, Michael B; Golden, Jeffrey A; LaBerge, Jeanne M; Webb, W Richard; Reddy, Gautham P; Wilson, Mark W; Kerlan, Robert K; Gordon, Roy L

    2002-01-01

    To determine the short- and long-term improvement in airflow dynamics in patients undergoing tracheobronchial stent placement for benign airway stenoses. Twenty-two patients underwent 34 tracheal and/or bronchial stent placement procedures for benign airway stenoses and had the results of pulmonary function tests available. Stent placement indications included bronchomalacia after lung transplantation (n = 11), postintubation stenoses (n = 6), relapsing polychondritis (n = 2), and 1 each of tracheomalacia, tracheal compression, and histoplasmosis. Six patients underwent more than one stent placement procedure (range: 2-7 procedures). The mean forced expiratory volume in one second (FEV(1) ), forced expiratory flow rate in the midportion of the forced vital capacity curve (FEF(25-75) ), forced vital capacity, and peak flow (PF) rate obtained before stent placement were compared with those immediately after stent placement and with those measurements most remote from stent placement using the paired two-tailed test. All patients reported improved respiratory function immediately after stent placement. The mean FEV(1), FEF(25-75), and PF rate improved significantly (p stent placement. On long-term follow-up averaging 15 months after stent placement, these parameters declined despite patients' subjective sense of improvement. Segregating the population into transplant and nontransplant airway stenosis etiologies, however, FEF(25-75) and PF rate remained significantly improved (p = 0.045, p = 0.027, respectively), over the long term for the latter. FEV increased after subsequent stent placements for patients receiving multiple stents. Stent placement for benign tracheobronchial stenoses provides significant immediate improvement in airflow dynamics. Long-term improvement in airflow obstruction may be expected, and additional stent placements may further improve pulmonary function.

  15. A short note on the paper of Liu et al. (2012). A relative Lempel-Ziv complexity: Application to comparing biological sequences. Chemical Physics Letters, volume 530, 19 March 2012, pages 107-112

    Science.gov (United States)

    Arit, Turkan; Keskin, Burak; Firuzan, Esin; Cavas, Cagin Kandemir; Liu, Liwei; Cavas, Levent

    2018-04-01

    The report entitled "L. Liu, D. Li, F. Bai, A relative Lempel-Ziv complexity: Application to comparing biological sequences, Chem. Phys. Lett. 530 (2012) 107-112" mentions on the powerful construction of phylogenetic trees based on Lempel-Ziv algorithm. On the other hand, the method explained in the paper does not give promising result on the data set on invasive Caulerpa taxifolia in the Mediterranean Sea. The phylogenetic trees are obtained by the proposed method of the aforementioned paper in this short note.

  16. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Two short basic sequences surrounding the zinc finger of nucleocapsid protein NCp10 of Moloney murine leukemia virus are critical for RNA annealing activity.

    Science.gov (United States)

    De Rocquigny, H; Ficheux, D; Gabus, C; Allain, B; Fournie-Zaluski, M C; Darlix, J L; Roques, B P

    1993-02-25

    The 56 amino acid nucleocapsid protein (NCp10) of Moloney Murine Leukemia Virus, contains a CysX2CysX4HisX4Cys zinc finger flanked by basic residues. In vitro NCp10 promotes genomic RNA dimerization, a process most probably linked to genomic RNA packaging, and replication primer tRNA(Pro) annealing to the initiation site of reverse transcription. To characterize the amino-acid sequences involved in the various functions of NCp10, we have synthesized by solid phase method the native protein and a series of derived peptides shortened at the N- or C-terminus with or without the zinc finger domain. In the latter case, the two parts of the protein were linked by a Glycine - Glycine spacer. The in vitro studies of these peptides show that nucleic acid annealing activities of NCp10 do not require a zinc finger but are critically dependent on the presence of specific sequences located on each side of the CCHC domain and containing proline and basic residues. Thus, deletion of 11R or 49PRPQT, of the fully active 29 residue peptide 11RQGGERRRSQLDRDGGKKPRGPRGPRPQT53 leads to a complete loss of NCp10 activity. Therefore it is proposed that in NCp10, the zinc finger directs the spatial recognition of the target RNAs by the basic domains surrounding the zinc finger.

  18. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity.

    Science.gov (United States)

    Costa, Marta D; Cherni, Lotfi; Fernandes, Verónica; Freitas, Fernando; Ammar El Gaaied, Amel Ben; Pereira, Luísa

    2009-04-01

    Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.

  19. Determination of the source of androgen excess in functionally atypical polycystic ovary syndrome by a short dexamethasone androgen-suppression test and a low-dose ACTH test.

    Science.gov (United States)

    Rosenfield, Robert L; Mortensen, Monica; Wroblewski, Kristen; Littlejohn, Elizabeth; Ehrmann, David A

    2011-11-01

    Polycystic ovary syndrome (PCOS) patients typically have 17-hydroxyprogesterone (17OHP) hyperresponsiveness to GnRH agonist (GnRHa) (PCOS-T). The objective of this study was to determine the source of androgen excess in the one-third of PCOS patients who atypically lack this type of ovarian dysfunction (PCOS-A). Aged-matched PCOS-T (n= 40), PCOS-A (n= 20) and controls (n= 39) were studied prospectively in a General Clinical Research Center. Short (4 h) and long (4-7 day) dexamethasone androgen-suppression tests (SDAST and LDAST, respectively) were compared in subsets of subjects. Responses to SDAST and low-dose adrenocorticotropic hormone (ACTH) were then evaluated in all. Testosterone post-SDAST correlated significantly with testosterone post-LDAST and 17OHP post-GnRHa (r = 0.671-0.672), indicating that all detect related aspects of ovarian dysfunction. An elevated dehydroepiandrosterone peak in response to ACTH, which defined functional adrenal hyperandrogenism, was similarly prevalent in PCOS-T (27.5%) and PCOS-A (30%) and correlated significantly with baseline dehydroepiandrosterone sulfate (DHEAS) (r = 0.708). Functional ovarian hyperandrogenism was detected by subnormal testosterone suppression by SDAST in most (92.5%) PCOS-T, but significantly fewer PCOS-A (60%, PPCOS-A, but present in 30% of PCOS-T (P PCOS-A cases with normal testosterone suppression in response to SDAST (5/8) lacked evidence of adrenal hyperandrogenism and were obese. Functional ovarian hyperandrogenism was not demonstrable by SDAST in 40% of PCOS-A. Most of these cases had no evidence of adrenal hyperandrogenism. Obesity may account for most hyperandrogenemic anovulation that lacks a glandular source of excess androgen, and the SDAST seems useful in making this distinction.

  20. Short-interval test-retest interrater reliability of the Dutch version of the structured clinical interview for DSM-IV personality disorders (SCID-II)

    NARCIS (Netherlands)

    Weertman, A; ArntZ, A; Dreessen, L; van Velzen, C; Vertommen, S

    2003-01-01

    This study examined the short-interval test-retest reliability of the Structured Clinical Interview (SCID-II: First, Spitzer, Gibbon, & Williams, 1995) for DSM-IV personality disorders (PDs). The SCID-II was administered to 69 in- and outpatients on two occasions separated by 1 to 6 weeks. The

  1. Two RNAs or DNAs May Artificially Fuse Together at a Short Homologous Sequence (SHS) during Reverse Transcription or Polymerase Chain Reactions, and Thus Reporting an SHS-Containing Chimeric RNA Requires Extra Caution

    Science.gov (United States)

    Xie, Bingkun; Yang, Wei; Ouyang, Yongchang; Chen, Lichan; Jiang, Hesheng; Liao, Yuying; Liao, D. Joshua

    2016-01-01

    Tens of thousands of chimeric RNAs have been reported. Most of them contain a short homologous sequence (SHS) at the joining site of the two partner genes but are not associated with a fusion gene. We hypothesize that many of these chimeras may be technical artifacts derived from SHS-caused mis-priming in reverse transcription (RT) or polymerase chain reactions (PCR). We cloned six chimeric complementary DNAs (cDNAs) formed by human mitochondrial (mt) 16S rRNA sequences at an SHS, which were similar to several expression sequence tags (ESTs).These chimeras, which could not be detected with cDNA protection assay, were likely formed because some regions of the 16S rRNA are reversely complementary to another region to form an SHS, which allows the downstream sequence to loop back and anneal at the SHS to prime the synthesis of its complementary strand, yielding a palindromic sequence that can form a hairpin-like structure.We identified a 16S rRNA that ended at the 4th nucleotide(nt) of the mt-tRNA-leu was dominant and thus should be the wild type. We also cloned a mouse Bcl2-Nek9 chimeric cDNA that contained a 5-nt unmatchable sequence between the two partners, contained two copies of the reverse primer in the same direction but did not contain the forward primer, making it unclear how this Bcl2-Nek9 was formed and amplified. Moreover, a cDNA was amplified because one primer has 4 nts matched to the template, suggesting that there may be many more artificial cDNAs than we have realized, because the nuclear and mt genomes have many more 4-nt than 5-nt or longer homologues. Altogether, the chimeric cDNAs we cloned are good examples suggesting that many cDNAs may be artifacts due to SHS-caused mis-priming and thus greater caution should be taken when new sequence is obtained from a technique involving DNA polymerization. PMID:27148738

  2. Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.

    Science.gov (United States)

    Mandelker, Diana; Zhang, Liying; Kemel, Yelena; Stadler, Zsofia K; Joseph, Vijai; Zehir, Ahmet; Pradhan, Nisha; Arnold, Angela; Walsh, Michael F; Li, Yirong; Balakrishnan, Anoop R; Syed, Aijazuddin; Prasad, Meera; Nafa, Khedoudja; Carlo, Maria I; Cadoo, Karen A; Sheehan, Meg; Fleischut, Megan H; Salo-Mullen, Erin; Trottier, Magan; Lipkin, Steven M; Lincoln, Anne; Mukherjee, Semanti; Ravichandran, Vignesh; Cambria, Roy; Galle, Jesse; Abida, Wassim; Arcila, Marcia E; Benayed, Ryma; Shah, Ronak; Yu, Kenneth; Bajorin, Dean F; Coleman, Jonathan A; Leach, Steven D; Lowery, Maeve A; Garcia-Aguilar, Julio; Kantoff, Philip W; Sawyers, Charles L; Dickler, Maura N; Saltz, Leonard; Motzer, Robert J; O'Reilly, Eileen M; Scher, Howard I; Baselga, Jose; Klimstra, David S; Solit, David B; Hyman, David M; Berger, Michael F; Ladanyi, Marc; Robson, Mark E; Offit, Kenneth

    2017-09-05

    Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of

  3. The earthquake sequence of 21-22 February, 1983 at Ramnicu Sarat, Romania: source parameters retrieved by short period local data inversion

    International Nuclear Information System (INIS)

    Ardeleanu, L.; Radulian, M.; Sileny, J.; Panza, G. F.

    2002-01-01

    High-frequency seismograms from the Romanian telemetered local network are inverted to retrieve the seismic moment tensor of five weak earthquakes (2.9 ≤ M L ≤ 3.6) belonging to the seismic sequence of Ramnicu Sarat (Romania) of 21-22 February 1983. A grossly simplified 1-D approximation of the crust - the horizontally layered inelastic earth model - is used to construct the Green's function by modal summation. The deviation from the real velocity structure originates the error in forward modelling, which is roughly estimated from the differences in the moment tensor rate functions obtained from subsets of the complete station network. This error is transformed into estimates of confidence regions of the time function, moment tensor and its principal axes, and error bars of the scalar moment. The 1-D approximation of the crust results in a large uncertainty of the source time function, which is almost completely undetermined. The mechanism is more confident, especially the determination of the orientation of its deviatoric part. The most robust source parameter from the three investigated items is the scalar moment. (authors)

  4. The intramuscular glucagon stimulation test does not provide good discrimination between normal and inadequate ACTH reserve when used in the investigation of short healthy children.

    Science.gov (United States)

    Tenenbaum, Ariel; Phillip, Moshe; de Vries, Liat

    2014-01-01

    Few studies have addressed the role of the glucagon stimulation test (GST) in evaluating the hypothalamic-pituitary-adrenal axis in children. We investigated the diagnostic value of the GST in evaluating the adrenocortical response in short healthy children. The GST was performed in 190 children investigated for short stature. A peak cortisol >500 nmol/l was considered a normal response. In the 45 (23.7%) with subnormal response, a 250-μg ACTH test was done. The rate of subnormal adrenal response to GST was higher among boys (33.9 vs. 8.9%, p 500 nmol/l in all the patients undergoing an ACTH stimulation test. Since adrenal response to GST is age- and gender-related and the false-positive rate is high, its routine performance in healthy children warrants reconsideration. © 2014 S. Karger AG, Basel.

  5. Simple construct evaluation with latent class analysis: An investigation of Facebook addiction and the development of a short form of the Facebook Addiction Test (F-AT).

    Science.gov (United States)

    Dantlgraber, Michael; Wetzel, Eunike; Schützenberger, Petra; Stieger, Stefan; Reips, Ulf-Dietrich

    2016-09-01

    In psychological research, there is a growing interest in using latent class analysis (LCA) for the investigation of quantitative constructs. The aim of this study is to illustrate how LCA can be applied to gain insights on a construct and to select items during test development. We show the added benefits of LCA beyond factor-analytic methods, namely being able (1) to describe groups of participants that differ in their response patterns, (2) to determine appropriate cutoff values, (3) to evaluate items, and (4) to evaluate the relative importance of correlated factors. As an example, we investigated the construct of Facebook addiction using the Facebook Addiction Test (F-AT), an adapted version of the Internet Addiction Test (I-AT). Applying LCA facilitates the development of new tests and short forms of established tests. We present a short form of the F-AT based on the LCA results and validate the LCA approach and the short F-AT with several external criteria, such as chatting, reading newsfeeds, and posting status updates. Finally, we discuss the benefits of LCA for evaluating quantitative constructs in psychological research.

  6. Validation of the Serpent 2-DYNSUB code sequence using the Special Power Excursion Reactor Test III (SPERT III)

    International Nuclear Information System (INIS)

    Knebel, Miriam; Mercatali, Luigi; Sanchez, Victor; Stieglitz, Robert; Macian-Juan, Rafael

    2016-01-01

    Highlights: • Full few-group cross section tables created by Monte Carlo lattice code Serpent 2. • Serpent 2 group constant methodology verified for HFP static and transient cases. • Serpent 2-DYNSUB tool chainvalidated using SPERT III REA experiments. • Serpent 2-DYNSUB tool chain suitable to model RIAs in PWRs. - Abstract: The Special Power Excursion Reactor Test III (SPERT III) is studied using the Serpent 2-DYNSUB code sequence in order to validate it for modeling reactivity insertion accidents (RIA) in PWRs. The SPERT III E-core was a thermal research reactor constructed to analyze reactor dynamics. Its configuration resembles a commercial PWR on terms of fuel type, choice of moderator, coolant flow and system pressure. The initial conditions of the rod ejection accident experiments (REA) performed cover cold startup, hot startup, hot standby and operating power scenarios. Eight of these experiments were analyzed in detail. Firstly, multi-dimensional nodal diffusion cross section tables were created for the three-dimensional reactor simulator DYNSUB employing the Monte Carlo neutron transport code Serpent 2. In a second step, DYNSUB stationary simulations were compared to Monte Carlo reference three-dimensional full scale solutions obtained with Serpent 2 (cold startup conditions) and Serpent 2/SUBCHANFLOW (operating power conditions) with a good agreement being observed. The latter tool is an internal coupling of Serpent 2 and the sub-channel thermal-hydraulics code SUBCHANFLOW. Finally, DYNSUB was utilized to study the eight selected transient experiments. Results were found to match measurements well. As the selected experiments cover much of the possible transient (delayed super-critical, prompt super-critical and super-prompt critical excursion) and initial conditions (cold and hot as well as zero, little and full power reactor states) one expects in commercial PWRs, the obtained results give confidence that the Serpent 2-DYNSUB tool chain is

  7. How to Say No: Single- and Dual-Process Theories of Short-Term Recognition Tested on Negative Probes

    Science.gov (United States)

    Oberauer, Klaus

    2008-01-01

    Three experiments with short-term recognition tasks are reported. In Experiments 1 and 2, participants decided whether a probe matched a list item specified by its spatial location. Items presented at study in a different location (intrusion probes) had to be rejected. Serial position curves of positive, new, and intrusion probes over the probed…

  8. Internal short circuit and accelerated rate calorimetry tests of lithium-ion cells: Considerations for methane-air intrinsic safety and explosion proof/flameproof protection methods.

    Science.gov (United States)

    Dubaniewicz, Thomas H; DuCarme, Joseph P

    2016-09-01

    Researchers with the National Institute for Occupational Safety and Health (NIOSH) studied the potential for lithium-ion cell thermal runaway from an internal short circuit in equipment for use in underground coal mines. In this third phase of the study, researchers compared plastic wedge crush-induced internal short circuit tests of selected lithium-ion cells within methane (CH 4 )-air mixtures with accelerated rate calorimetry tests of similar cells. Plastic wedge crush test results with metal oxide lithium-ion cells extracted from intrinsically safe evaluated equipment were mixed, with one cell model igniting the chamber atmosphere while another cell model did not. The two cells models exhibited different internal short circuit behaviors. A lithium iron phosphate (LiFePO 4 ) cell model was tolerant to crush-induced internal short circuits within CH 4 -air, tested under manufacturer recommended charging conditions. Accelerating rate calorimetry tests with similar cells within a nitrogen purged 353-mL chamber produced ignitions that exceeded explosion proof and flameproof enclosure minimum internal pressure design criteria. Ignition pressures within a 20-L chamber with 6.5% CH 4 -air were relatively low, with much larger head space volume and less adiabatic test conditions. The literature indicates that sizeable lithium thionyl chloride (LiSOCl 2 ) primary (non rechargeable) cell ignitions can be especially violent and toxic. Because ignition of an explosive atmosphere is expected within explosion proof or flameproof enclosures, there is a need to consider the potential for an internal explosive atmosphere ignition in combination with a lithium or lithium-ion battery thermal runaway process, and the resulting effects on the enclosure.

  9. Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.

    Science.gov (United States)

    Ben-David, Smadar; Yaakov, Beery; Kashkush, Khalil

    2013-10-01

    Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retroelements that are present in most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (Triticum aestivum). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454 pyrosequencing database of T. aestivum. In addition, we utilized site-specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We retrieved 3706 different insertions of Au SINE from the 454 pyrosequencing database of T. aestivum, and found that most of the elements are inserted in A/T-rich regions, while approximately 38% of the insertions are associated with transcribed regions, including known wheat genes. We observed typical retrotransposition of Au SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid Triticum and Aegilops species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of Au SINE in the first four generations for two of three newly formed allopolyploid species used in this study. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress-induced activation. © 2013 Ben-Gurion University The Plant Journal © 2013 John Wiley & Sons Ltd.

  10. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

    Science.gov (United States)

    Stark, Zornitza; Tan, Tiong Y; Chong, Belinda; Brett, Gemma R; Yap, Patrick; Walsh, Maie; Yeung, Alison; Peters, Heidi; Mordaunt, Dylan; Cowie, Shannon; Amor, David J; Savarirayan, Ravi; McGillivray, George; Downie, Lilian; Ekert, Paul G; Theda, Christiane; James, Paul A; Yaplito-Lee, Joy; Ryan, Monique M; Leventer, Richard J; Creed, Emma; Macciocca, Ivan; Bell, Katrina M; Oshlack, Alicia; Sadedin, Simon; Georgeson, Peter; Anderson, Charlotte; Thorne, Natalie; Melbourne Genomics Health Alliance; Gaff, Clara; White, Susan M

    2016-11-01

    To prospectively evaluate the diagnostic and clinical utility of singleton whole-exome sequencing (WES) as a first-tier test in infants with suspected monogenic disease. Singleton WES was performed as a first-tier sequencing test in infants recruited from a single pediatric tertiary center. This occurred in parallel with standard investigations, including single- or multigene panel sequencing when clinically indicated. The diagnosis rate, clinical utility, and impact on management of singleton WES were evaluated. Of 80 enrolled infants, 46 received a molecular genetic diagnosis through singleton WES (57.5%) compared with 11 (13.75%) who underwent standard investigations in the same patient group. Clinical management changed following exome diagnosis in 15 of 46 diagnosed participants (32.6%). Twelve relatives received a genetic diagnosis following cascade testing, and 28 couples were identified as being at high risk of recurrence in future pregnancies. This prospective study provides strong evidence for increased diagnostic and clinical utility of singleton WES as a first-tier sequencing test for infants with a suspected monogenic disorder. Singleton WES outperformed standard care in terms of diagnosis rate and the benefits of a diagnosis, namely, impact on management of the child and clarification of reproductive risks for the extended family in a timely manner.Genet Med 18 11, 1090-1096.

  11. Quiet Clean Short-Haul Experimental Engine (QCSEE) ball spline pitch-change mechanism whirligig test report

    Science.gov (United States)

    1978-01-01

    The component testing of a ball spline variable pitch mechanism is described including a whirligig test. The variable pitch actuator successfully completed all planned whirligig tests including a fifty cycle endurance test at actuation rates up to 125 deg per second at up to 102 percent fan speed (3400 rpm).

  12. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

    Directory of Open Access Journals (Sweden)

    Haznedaroglu Berat Z

    2012-07-01

    Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities

  13. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

    Directory of Open Access Journals (Sweden)

    Greenblatt Jack

    2006-07-01

    included in genome-wide yeast TAP tagging projects. Conclusion PIPE analysis can predict yeast protein-protein interactions. Also, PIPE analysis can be used to study the internal architecture of yeast protein complexes. The data also suggests that a finite set of short polypeptide signals seem to be responsible for the majority of the yeast protein-protein interactions.

  14. MK-801 and memantine act differently on short-term memory tested with different time-intervals in the Morris water maze test

    Czech Academy of Sciences Publication Activity Database

    Duda, W.; Wesierska, M.; Ostaszewski, P.; Valeš, Karel; Nekovářová, Tereza; Stuchlík, Aleš

    2016-01-01

    Roč. 311, Sep 15 (2016), s. 15-23 ISSN 0166-4328 R&D Projects: GA MŠk(CZ) LH14053; GA ČR(CZ) GA14-03627S Institutional support: RVO:67985823 Keywords : short-term memory * spatial working memory * memantine * dizocilpine * Morris water maze Subject RIV: FH - Neurology Impact factor: 3.002, year: 2016

  15. Testing of Commercial Milk Production Technology Using A Combination of High Temperature Short Time and Pulsed Electric Field

    OpenAIRE

    Hadi A; Widjanarko SB; Kusnadi J

    2016-01-01

    The development of milk processing technology has grown excessively, and it contains advantage and disadvantage. This study used mixed between PEF (Pulsed Electric Field) and High Temperature Short Time (HTST) to produce milk processed product which is effective and efficient in killing milk microorganism without changing its color, scent, and nutrient content of processed product, therefore producing commercial sterile milk product in accord with milk Indonesian National Standard (SNI). The ...

  16. The first FDA marketing authorizations of next-generation sequencing technology and tests: challenges, solutions and impact for future assays.

    Science.gov (United States)

    Bijwaard, Karen; Dickey, Jennifer S; Kelm, Kellie; Težak, Živana

    2015-01-01

    The rapid emergence and clinical translation of novel high-throughput sequencing technologies created a need to clarify the regulatory pathway for the evaluation and authorization of these unique technologies. Recently, the US FDA authorized for marketing four next generation sequencing (NGS)-based diagnostic devices which consisted of two heritable disease-specific assays, library preparation reagents and a NGS platform that are intended for human germline targeted sequencing from whole blood. These first authorizations can serve as a case study in how different types of NGS-based technology are reviewed by the FDA. In this manuscript we describe challenges associated with the evaluation of these novel technologies and provide an overview of what was reviewed. Besides making validated NGS-based devices available for in vitro diagnostic use, these first authorizations create a regulatory path for similar future instruments and assays.

  17. A test of Monroe's Motivated Sequence for its effects on ratings of message organization and attitude change.

    Science.gov (United States)

    Micciche, T; Pryor, B; Butler, J

    2000-06-01

    The experiment examined Monroe's Motivated Sequence, an organizational pattern commonly taught in basic speech courses for its effects on attitude change and ratings of comprehensibility of messages. Treatment groups of 21, 23, and 24 participants read one of three versions of a persuasive message that advocated a $50 fee increase to improve parking facilities on campus. One version represented Monroe's five-step sequence, a second version reversed the five steps, and a third randomly ordered the steps. A control group of 22 read a message unrelated to the parking issue. Analysis showed no differences in attitude change across the four groups. The Monroe sequence condition did produce significantly higher ratings of comprehensibility on one of four comparisons.

  18. A short-form version of the Boston Naming Test for language screening in dementia in a bilingual rural community in Galicia (Spain).

    Science.gov (United States)

    Nebreda, M C; García-Caballero, A; Asensio, E; Revilla, P; Rodriguez-Girondo, M; Mateos, R

    2011-04-01

    Aphasia, one of the core symptoms of cortical dementia, is routinely evaluated using graded naming tests like the Boston Naming Test (BNT). However, the application of this 60-item test is time-consuming and shortened versions have been devised for screening. The hypothesis of this research is that a specifically designed shortened version of the BNT could replace the original 60-item BNT as part of a mini-battery for screening for dementia. The objective of this study was to design a short version of the BNT for a rural population in Galicia (Spain). A clinic group of 102 patients including 43 with dementia was recruited along with 78 healthy volunteers. The clinic and control groups were scored on the Spanish version of the Mini-mental State Examination (MMSE) and BNT. In addition, the clinic group was tested with standard neuropsychological instruments and underwent brain investigations and routine neurological examination. BNT items with specificity and sensitivity above 0.5 were selected to compose a short battery of 11 pictures named BNTOu11. ANOVA and mean comparisons were made for MMSE and BNT versions. Receiver operating characteristics (ROC) curves and internal consistency were calculated. Areas under ROC curves (AUC) did not show statistically significant differences; therefore BNTOu11's AUC (0.814) was similar to the 60-item BNT versions (0.785 and 0.779), to the short versions from Argentina (0.772) and Andalusia (0.799) and to the Spanish MMSE (0.866). BNTOu11 had higher internal consistency than the other short versions. BNTOu11 is a useful and time-saving method as part of a battery for screening for dementia in a psychogeriatric outpatient unit.

  19. Short-term adhesion and long-term biofouling testing of polydopamine and poly(ethylene glycol) surface modifications of membranes and feed spacers for biofouling control

    KAUST Repository

    Miller, Daniel J.

    2012-08-01

    Ultrafiltration, nanofiltration membranes and feed spacers were hydrophilized with polydopamine and polydopamine- g-poly(ethylene glycol) surface coatings. The fouling propensity of modified and unmodified membranes was evaluated by short-term batch protein and bacterial adhesion tests. The fouling propensity of modified and unmodified membranes and spacers was evaluated by continuous biofouling experiments in a membrane fouling simulator. The goals of the study were: 1) to determine the effectiveness of polydopamine and polydopamine- g-poly(ethylene glycol) membrane coatings for biofouling control and 2) to compare techniques commonly used in assessment of membrane biofouling propensity with biofouling experiments under practical conditions. Short-term adhesion tests were carried out under static, no-flow conditions for 1 h using bovine serum albumin, a common model globular protein, and Pseudomonas aeruginosa, a common model Gram-negative bacterium. Biofouling tests were performed in a membrane fouling simulator (MFS) for several days under flow conditions similar to those encountered in industrial modules with the autochthonous drinking water population and acetate dosage as organic substrate. Polydopamine- and polydopamine- g-poly(ethylene glycol)-modified membranes showed significantly reduced adhesion of bovine serum albumin and P. aeruginosa in the short-term adhesion tests, but no reduction of biofouling was observed during longer biofouling experiments with modified membranes and spacers. These results demonstrate that short-term batch adhesion experiments using model proteins or bacteria under static conditions are not indicative of biofouling, while continuous biofouling experiments showed that membrane surface modification by polydopamine and polydopamine- g-poly(ethylene glycol) is not effective for biofouling control. © 2012 Elsevier Ltd.

  20. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Directory of Open Access Journals (Sweden)

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  1. Testing for the validity of purchasing power parity theory both in the long-run and the short-run for ASEAN-5

    Science.gov (United States)

    Choji, Niri Martha; Sek, Siok Kun

    2017-11-01

    The purchasing power parity theory says that the trade rates among two nations ought to be equivalent to the proportion of the total price levels between the two nations. For more than a decade, there has been substantial interest in testing for the validity of the Purchasing Power Parity (PPP) empirically. This paper performs a series of tests to see if PPP is valid for ASEAN-5 nations for the period of 2000-2016 using monthly data. For this purpose, we conducted four different tests of stationarity, two cointegration tests (Pedroni and Westerlund), and also the VAR model. The stationarity (unit root) tests reveal that the variables are not stationary at levels however stationary at first difference. Cointegration test results did not reject the H0 of no cointegration implying the absence long-run association among the variables and results of the VAR model did not reveal a strong short-run relationship. Based on the data, we, therefore, conclude that PPP is not valid in long-and short-run for ASEAN-5 during 2000-2016.

  2. Fat suppression with short inversion time inversion-recovery and chemical-shift selective saturation: a dual STIR-CHESS combination prepulse for turbo spin echo pulse sequences.

    Science.gov (United States)

    Tanabe, Koji; Nishikawa, Keiichi; Sano, Tsukasa; Sakai, Osamu; Jara, Hernán

    2010-05-01

    To test a newly developed fat suppression magnetic resonance imaging (MRI) prepulse that synergistically uses the principles of fat suppression via inversion recovery (STIR) and spectral fat saturation (CHESS), relative to pure CHESS and STIR. This new technique is termed dual fat suppression (Dual-FS). To determine if Dual-FS could be chemically specific for fat, the phantom consisted of the fat-mimicking NiCl(2) aqueous solution, porcine fat, porcine muscle, and water was imaged with the three fat-suppression techniques. For Dual-FS and STIR, several inversion times were used. Signal intensities of each image obtained with each technique were compared. To determine if Dual-FS could be robust to magnetic field inhomogeneities, the phantom consisting of different NiCl(2) aqueous solutions, porcine fat, porcine muscle, and water was imaged with Dual-FS and CHESS at the several off-resonance frequencies. To compare fat suppression efficiency in vivo, 10 volunteer subjects were also imaged with the three fat-suppression techniques. Dual-FS could suppress fat sufficiently within the inversion time of 110-140 msec, thus enabling differentiation between fat and fat-mimicking aqueous structures. Dual-FS was as robust to magnetic field inhomogeneities as STIR and less vulnerable than CHESS. The same results for fat suppression were obtained in volunteers. The Dual-FS-STIR-CHESS is an alternative and promising fat suppression technique for turbo spin echo MRI. Copyright 2010 Wiley-Liss, Inc.

  3. The BACHD Rat Model of Huntington Disease Shows Signs of Fronto-Striatal Dysfunction in Two Operant Conditioning Tests of Short-Term Memory.

    Directory of Open Access Journals (Sweden)

    Erik Karl Håkan Clemensson

    Full Text Available The BACHD rat is a recently developed transgenic animal model of Huntington disease, a progressive neurodegenerative disorder characterized by extensive loss of striatal neurons. Cognitive impairments are common among patients, and characterization of similar deficits in animal models of the disease is therefore of interest. The present study assessed the BACHD rats' performance in the delayed alternation and the delayed non-matching to position test, two Skinner box-based tests of short-term memory function. The transgenic rats showed impaired performance in both tests, indicating general problems with handling basic aspects of the tests, while short-term memory appeared to be intact. Similar phenotypes have been found in rats with fronto-striatal lesions, suggesting that Huntington disease-related neuropathology might be present in the BACHD rats. Further analyses indicated that the performance deficit in the delayed alternation test might be due to impaired inhibitory control, which has also been implicated in Huntington disease patients. The study ultimately suggests that the BACHD rats might suffer from neuropathology and cognitive impairments reminiscent of those of Huntington disease patients.

  4. The BACHD Rat Model of Huntington Disease Shows Signs of Fronto-Striatal Dysfunction in Two Operant Conditioning Tests of Short-Term Memory.

    Science.gov (United States)

    Clemensson, Erik Karl Håkan; Clemensson, Laura Emily; Riess, Olaf; Nguyen, Huu Phuc

    2017-01-01

    The BACHD rat is a recently developed transgenic animal model of Huntington disease, a progressive neurodegenerative disorder characterized by extensive loss of striatal neurons. Cognitive impairments are common among patients, and characterization of similar deficits in animal models of the disease is therefore of interest. The present study assessed the BACHD rats' performance in the delayed alternation and the delayed non-matching to position test, two Skinner box-based tests of short-term memory function. The transgenic rats showed impaired performance in both tests, indicating general problems with handling basic aspects of the tests, while short-term memory appeared to be intact. Similar phenotypes have been found in rats with fronto-striatal lesions, suggesting that Huntington disease-related neuropathology might be present in the BACHD rats. Further analyses indicated that the performance deficit in the delayed alternation test might be due to impaired inhibitory control, which has also been implicated in Huntington disease patients. The study ultimately suggests that the BACHD rats might suffer from neuropathology and cognitive impairments reminiscent of those of Huntington disease patients.

  5. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  6. Evaluation of T2-weighted versus short-tau inversion recovery sagittal sequences in the identification and localization of canine intervertebral disc extrusion with low-field magnetic resonance imaging.

    Science.gov (United States)

    Housley, Daniel; Caine, Abby; Cherubini, Giunio; Taeymans, Olivier

    2017-07-01

    Sagittal T2-weighted sequences (T2-SAG) are the foundation of spinal protocols when screening for the presence of intervertebral disc extrusion. We often utilize sagittal short-tau inversion recovery sequences (STIR-SAG) as an adjunctive screening series, and experience suggests that this combined approach provides superior detection rates. We hypothesized that STIR-SAG would provide higher sensitivity than T2-SAG in the identification and localization of intervertebral disc extrusion. We further hypothesized that the parallel evaluation of paired T2-SAG and STIR-SAG series would provide a higher sensitivity than could be achieved with either independent sagittal series when viewed in isolation. This retrospective diagnostic accuracy study blindly reviewed T2-SAG and STIR-SAG sequences from dogs (n = 110) with surgically confirmed intervertebral disc extrusion. A consensus between two radiologists found no significant difference in sensitivity between T2-SAG and STIR-SAG during the identification of intervertebral disc extrusion (T2-SAG: 92.7%, STIR-SAG: 94.5%, P = 0.752). Nevertheless, STIR-SAG accurately identified intervertebral disc extrusion in 66.7% of cases where the evaluation of T2-SAG in isolation had provided a false negative diagnosis. Additionally, one radiologist found that the parallel evaluation of paired T2-SAG and STIR-SAG series provided a significantly higher sensitivity than T2-SAG in isolation, during the identification of intervertebral disc extrusion (T2-SAG: 78.2%, paired T2-SAG, and STIR-SAG: 90.9%, P = 0.017). A similar nonsignificant trend was observed when the consensus of both radiologists was taken into consideration (T2-SAG: 92.7%, paired T2-SAG, and STIR-SAG = 97.3%, P = 0.392). We therefore conclude that STIR-SAG is capable of identifying intervertebral disc extrusion that is inconspicuous in T2-SAG, and that STIR-SAG should be considered a useful adjunctive sequence during preliminary sagittal screening for intervertebral disc

  7. Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.

    Science.gov (United States)

    Shin, Saeam; Kim, Yoonjung; Chul Oh, Seoung; Yu, Nae; Lee, Seung-Tae; Rak Choi, Jong; Lee, Kyung-A

    2017-05-23

    In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.

  8. Progress in the development of short term chronic toxicity testing methods for crude oil and commercial bioremediation agents

    International Nuclear Information System (INIS)

    Cavender, R.C.; Cherry, D.S.; Dobbs, M.G.; Bidwell, J.R.; Yeager, M.M.

    1995-01-01

    Proposed modifications to the National Oil and Hazardous Substance Pollution Contingency Plan (NCP) have prompted examinations of the methodology used in toxicity testing of the water soluble fraction of oil, commercial bioremediation agents (CBA), and a combination of the two. The specific concerns addressed by this research are the use of unweathered Alaska North Slope (ANS) crude oil instead of the more expensive, less environmentally realistic distillate ANS-521, and the appropriate laboratory preparation methodology for the water soluble fraction (WSF) used in testing. Seven-day chronic tests exposing the inland silverside (Menidia beryllina) and estuarine mysid (Mysidopsis bahia) to the water soluble fraction of unweathered ANS and ANS-521 showed that mysids responded similarly to the two types of oils while silversides were more sensitive to unweathered ANS. In the presence of a CBA and WSF, the mortality of the organisms and the mysid growth were similar in both types of oil. The NOEC for silverside growth, however, was lower in the combined exposure of a CBA with ANS-521 WSF than it was in the CBA-WSF unweathered ANS. Testing is underway to determine if the stirring time length effects the toxicity of the WSF, or the WSF and CBA combination. In chronic tests using both the silverside and mysid there were no differences in growth and mortality of the organisms tested in WSF prepared from 10 and 20 hours of stirring, however, the 5 hour stirring exposure is less toxic to both organisms

  9. Short message service reminder intervention doubles sexually transmitted infection/HIV re-testing rates among men who have sex with men.

    Science.gov (United States)

    Bourne, C; Knight, V; Guy, R; Wand, H; Lu, H; McNulty, A

    2011-04-01

    To evaluate the impact of a short message service (SMS) reminder system on HIV/sexually transmitted infection (STI) re-testing rates among men who have sex with men (MSM). The SMS reminder programme started in late 2008 at a large Australian sexual health clinic. SMS reminders were recommended 3-6 monthly for MSM considered high-risk based on self-reported sexual behaviour. The evaluation compared HIV negative MSM who had a HIV/STI test between 1 January and 31 August 2010 and received a SMS reminder (SMS group) with those tested in the same time period (comparison group) and pre-SMS period (pre-SMS group, 1 January 2008 and 31 August 2008) who did not receive the SMS. HIV/STI re-testing rates were measured within 9 months for each group. Baseline characteristics were compared between study groups and multivariate logistic regression used to assess the association between SMS and re-testing and control for any imbalances in the study groups. There were 714 HIV negative MSM in the SMS group, 1084 in the comparison group and 1753 in the pre-SMS group. In the SMS group, 64% were re-tested within 9 months compared to 30% in the comparison group (preminders increased HIV/STI re-testing among HIV negative MSM. SMS offers a cheap, efficient system to increase HIV/STI re-testing in a busy clinical setting.

  10. Towards Point-of-Care Diagnosis of Pulmonary Tuberculosis and Drug Susceptibility Testing by Whole Genome Sequencing of DNA Isolated from Sputum

    Directory of Open Access Journals (Sweden)

    Kayzad S. Nilgiriwala

    2017-12-01

    Full Text Available Preliminary screening of pulmonary tuberculosis (TB in India still relies on sputum microscopy, which has low sensitivity leading to high rate of false negatives. Moreover, conventional phenotypic drug susceptibility testing (DST is conducted over a period of weeks leading to delays in correct treatment. Next generation sequencing technologies (Illumina and Oxford Nanopore have made it possible to sequence miniscule amount of DNA and generate enough data within a day for detecting specific microbes and their DST profile. Sputum samples from two pulmonary TB patients were processed by decontamination and DNA was isolated from the decontaminated sputum sediments. The isolated DNA was used for sequencing by Illumina and by MinION (Oxford Nanopore Technologies. The sequence data was used to diagnose TB and to determine the DST profiles for the first- and second-line drugs by Mykrobe Predictor. Validation was conducted by sequencing DNA (by Illumina isolated from pure growth culture from both the samples individually. DNA sequencing data (for both, Ilumina and MinION from one of the sputum samples indicated the presence of Mycobacterium tuberculosis (M. tb resistant to streptomycin, isoniazid, rifampicin and ethambutol and its lineage was predicted to be Beijing East Asia. The second sample indicated the presence of M. tb sensitive to the first- and second-line drugs by MinION and showed minor resistance call only to rifampicin by Illumina. Lineage of the second sample was predicted to be East Africa Indian Ocean, whereas Illumina data indicated it to be Delhi Central Asia. The two samples were correctly diagnosed for the presence of M. tb in the sputum DNA. Their DST profiles and lineage were also successfully determined from both the sequencing platforms (with minor discrepancies paving the way towards diagnosis and DST of TB from DNA isolated from sputum samples at point-of-care. Nanopore sequencing currently requires skilled personnel for DNA

  11. Development and testing of a CW-EPR apparatus for imaging of short-lifetime nitroxyl radicals in mouse head

    Science.gov (United States)

    Sato-Akaba, Hideo; Fujii, Hirotada; Hirata, Hiroshi

    2008-08-01

    This article describes a method for reducing the acquisition time in three-dimensional (3D) continuous-wave electron paramagnetic resonance (CW-EPR) imaging. To visualize nitroxyl spin probes, which have a short lifetime in living organisms, the acquisition time for a data set of spectral projections should be shorter than the lifetime of the spin probes. To decrease the total time required for data acquisition, the duration of magnetic field scanning was reduced to 0.5 s. Moreover, the number of projections was decreased by using the concept of a uniform distribution. To demonstrate this faster data acquisition, two kinds of nitroxyl radicals with different decay rates were measured in mice. 3D EPR imaging of 4-hydroxy-2,2,6,6-tetramethylpiperidine-d 17-1- 15N-1-oxyl in mouse head was successfully carried out. 3D EPR imaging of nitroxyl spin probes with a half-life of a few minutes was achieved for the first time in live animals.

  12. Strengthened effective connectivity underlies transfer of working memory training to tests of short-term memory and attention.

    Science.gov (United States)

    Kundu, Bornali; Sutterer, David W; Emrich, Stephen M; Postle, Bradley R

    2013-05-15

    Although long considered a natively endowed and fixed trait, working memory (WM) ability has recently been shown to improve with intensive training. What remains controversial and poorly understood, however, are the neural bases of these training effects and the extent to which WM training gains transfer to other cognitive tasks. Here we present evidence from human electrophysiology (EEG) and simultaneous transcranial magnetic stimulation and EEG that the transfer of WM training to other cognitive tasks is supported by changes in task-related effective connectivity in frontoparietal and parieto-occipital networks that are engaged by both the trained and transfer tasks. One consequence of this effect is greater efficiency of stimulus processing, as evidenced by changes in EEG indices of individual differences in short-term memory capacity and in visual search performance. Transfer to search-related activity provides evidence that something more fundamental than task-specific strategy or stimulus-specific representations has been learned. Furthermore, these patterns of training and transfer highlight the role of common neural systems in determining individual differences in aspects of visuospatial cognition.

  13. Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-analysis of Noncoding Variation in Metabochip Data.

    Science.gov (United States)

    He, Zihuai; Xu, Bin; Lee, Seunggeun; Ionita-Laza, Iuliana

    2017-09-07

    Substantial progress has been made in the functional annotation of genetic variation in the human genome. Integrative analysis that incorporates such functional annotations into sequencing studies can aid the discovery of disease-associated genetic variants, especially those with unknown function and located outside protein-coding regions. Direct incorporation of one functional annotation as weight in existing dispersion and burden tests can suffer substantial loss of power when the functional annotation is not predictive of the risk status of a variant. Here, we have developed unified tests that can utilize multiple functional annotations simultaneously for integrative association analysis with efficient computational techniques. We show that the proposed tests significantly improve power when variant risk status can be predicted by functional annotations. Importantly, when functional annotations are not predictive of risk status, the proposed tests incur only minimal loss of power in relation to existing dispersion and burden tests, and under certain circumstances they can even have improved power by learning a weight that better approximates the underlying disease model in a data-adaptive manner. The tests can be constructed with summary statistics of existing dispersion and burden tests for sequencing data, therefore allowing meta-analysis of multiple studies without sharing individual-level data. We applied the proposed tests to a meta-analysis of noncoding rare variants in Metabochip data on 12,281 individuals from eight studies for lipid traits. By incorporating the Eigen functional score, we detected significant associations between noncoding rare variants in SLC22A3 and low-density lipoprotein and total cholesterol, associations that are missed by standard dispersion and burden tests. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  14. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Directory of Open Access Journals (Sweden)

    Luís França

    Full Text Available Over a period of ten months a total of 5618 cord blood units (CBU were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  15. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Science.gov (United States)

    França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S

    2015-01-01

    Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  16. Beryllium abundances along the evolutionary sequence of the open cluster IC 4651 - A new test for hydrodynamical stellar models

    Science.gov (United States)

    Smiljanic, R.; Pasquini, L.; Charbonnel, C.; Lagarde, N.

    2010-02-01

    Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims: Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods: Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results: Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the

  17. A Measure of Proficiency or Short-Term Memory? Validation of an Elicited Imitation Test for SLA Research

    Science.gov (United States)

    Kim, Youjin; Tracy-Ventura, Nicole; Jung, Yeonjoo

    2016-01-01

    Elicited imitation requires listeners to listen and repeat sentences as accurately as possible. In second language acquisition (SLA) research it has been used for a variety of purposes. Recently, versions of the same elicited imitation test (EIT) have been created in 6 languages with the purpose of measuring second language proficiency (Ortega…

  18. An investigation of the genetic toxicology of irradiated food-stuffs using short-term test systems

    International Nuclear Information System (INIS)

    Renner, H.W.; Altmann, H.; Asquith, J.C.; Elias, P.S.

    1982-01-01

    Six in vivo genetic toxicity tests were carried out on irradiated or unirradiated cooked chicken, dried dates and cooked fish. The tests were as follows: sex-linked recessive lethal mutations in Drosophila melanogaster (dried dates only), chromosome aberrations in bone marrow of Chinese hamsters, micronucleus test in rats, mice and Chinese hamsters, sister-chromatid exchange in bone marrow of mice and Chinese hamsters and in spermatogonia of mice, and DNA metabolism in spleen cells of Chinese hamsters. None of the tests provided any evidence of genetic toxicity induced by irradiation. However, dried dates, whether irradiated or not, showed evidence of some genetic toxicity in their effect on DNA metabolism in spleen cells and SCE induction in bone marrow. Feeding irradiated fish affected DNA metabolism in the spleen cells of Chinese hamsters. This effect could be interpreted as an induction of an immunoactive compound, although it could also be explained by the persistence of an immunoactive compound due to the removal by irradiation of spoilage organisms that would normally degrade it. (author)

  19. Clinical Utility of Short Social Cognitive Tests in Early Differentiation of Behavioral Variant Frontotemporal Dementia from Alzheimer’s Disease

    DEFF Research Database (Denmark)

    Buhl, Christian; Stokholm, Jette; Gade, Anders

    2013-01-01

    Traditional cognitive tests used in clinical practice may not be sensitive enough for the early differentiation of behavioral variant frontotemporal dementia (bvFTD) from Alzheimer's disease (AD). A growing body of literature has shown that deficits in various aspects of social cognition can be f...

  20. The Effects of Tacrolimus on T-Cell Proliferation Are Short-Lived: A Pilot Analysis of Immune Function Testing

    Directory of Open Access Journals (Sweden)

    Benjamin L. Laskin, MD, MS

    2017-08-01

    Conclusions. T-cell proliferation is currently not suitable to measure immunosuppression because sample processing diminishes observable effects. Future immune function testing should focus on fresh samples with minimal washing steps. Our results also emphasize the importance of adherence to immunosuppressive treatment, because T-cell proliferation recovered substantially after even brief discontinuation of tacrolimus.

  1. Summary of Test Results of MQXFS1—The First Short Model 150 mm Aperture Nb$_3$Sn Quadrupole for the High-Luminosity LHC Upgrade

    CERN Document Server

    Stoynev, S; Anerella, M; Bossert, R; Cavanna, E; Cheng, D; Dietderich, D; DiMarco, J; Felice, H; Ferracin, P; Chlachidze, G; Ghosh, A; Grosclaude, P; Guinchard, M; Hafalia, A R; Holik, E; Izquierdo Bermudez, S; Krave, S; Marchevsky, M; Nobrega, F; Orris, D; Pan, H; Perez, J C; Prestemon, S; Ravaioli, E; Sabbi, G; Salmi, T; Schmalzle, J; Strauss, T; Sylvester, C; Tartaglia, M; Todesco, E; Vallone, G; Velev, G; Wanderer, P; Wang, X; Yu, M

    2017-01-01

    The development of $Nb_3Sn$ quadrupole magnets for the High-Luminosity LHC upgrade is a joint venture between the US LHC Accelerator Research Program (LARP)* and CERN with the goal of fabricating large aperture quadrupoles for the LHC in-teraction regions (IR). The inner triplet (low-β) NbTi quadrupoles in the IR will be replaced by the stronger Nb$_{3}$Sn magnets boosting the LHC program of having 10-fold increase in integrated luminos-ity after the foreseen upgrades. Previously LARP conducted suc-cessful tests of short and long models with up to 120 mm aperture. The first short 150 mm aperture quadrupole model MQXFS1 was assembled with coils fabricated by both CERN and LARP. The magnet demonstrated strong performance at the Fermilab’s verti-cal magnet test facility reaching the LHC operating limits. This paper reports the latest results from MQXFS1 tests with changed pre-stress levels. The overall magnet performance, including quench training and memory, ramp rate and temperature depend-ence, is also sum...

  2. Summary of Test Results of MQXFS1 - The First Short Model 150 mm Aperture $Nb_3Sn$ Quadrupole for the High-Luminosity

    Energy Technology Data Exchange (ETDEWEB)

    Stoynev, S.; et al.

    2017-01-01

    The development of $Nb_3Sn$ quadrupole magnets for the High-Luminosity LHC upgrade is a joint venture between the US LHC Accelerator Research Program (LARP)* and CERN with the goal of fabricating large aperture quadrupoles for the LHC in-teraction regions (IR). The inner triplet (low-β) NbTi quadrupoles in the IR will be replaced by the stronger Nb3Sn magnets boosting the LHC program of having 10-fold increase in integrated luminos-ity after the foreseen upgrades. Previously LARP conducted suc-cessful tests of short and long models with up to 120 mm aperture. The first short 150 mm aperture quadrupole model MQXFS1 was assembled with coils fabricated by both CERN and LARP. The magnet demonstrated strong performance at the Fermilab’s verti-cal magnet test facility reaching the LHC operating limits. This paper reports the latest results from MQXFS1 tests with changed pre-stress levels. The overall magnet performance, including quench training and memory, ramp rate and temperature depend-ence, is also summarized.

  3. Use of micro-tomography for validation of method to identify interfacial shear strength from tensile tests of short regenerated cellulose fibre composites

    DEFF Research Database (Denmark)

    Hajlane, A.; Miettinen, A.; Madsen, Bo

    2016-01-01

    The interfacial shear strength of short regenerated cellulose fibre/polylactide composites was characterized by means of an industry-friendly adhesion test method. The interfacial shear strength was back-calculated from the experimental tensile stress-strain curves of composites by using a micro......-mechanical model. The parameters characterizing the microstructure of the composites, e.g. fibre length and orientation distributions, used as input in the model were obtained by micro-tomography. The investigation was carried out on composites with untreated and surface treated fibres with various fibre weight...

  4. Solid oxide fuel cell short stack performance testing - Part A: Experimental analysis and μ-combined heat and power unit comparison

    Science.gov (United States)

    Mastropasqua, L.; Campanari, S.; Brouwer, J.

    2017-12-01

    The need to experimentally understand the detailed performance of SOFC stacks under operating conditions typical of commercial SOFC systems has prompted this two-part study. The steady state performance of a 6-cell short stack of yttria (Y2O3) stabilised zirconia (YSZ) with Ni/YSZ anodes and composite Sr-doped lanthanum manganite (LaMnO3, LSM)/YSZ cathodes is experimentally evaluated. In Part A, the stack characterisation is carried out by means of sensitivity analyses on the fuel utilisation factor and the steam-to-carbon ratio. Electrical and environmental performances are assessed and the results are compared with a commercial full-scale micro-CHP system, which comprises the same cells. The results show that the measured temperature dynamics of the short stack in a test stand environment are on the order of many minutes; therefore, one cannot neglect temperature dynamics for a precise measurement of the steady state polarisation behaviour. The overall polarisation performance is comparable to that of the full stack employed in the micro-CHP system, confirming the good representation that short-stack analyses can give of the entire SOFC module. The environmental performance is measured verifying the negligible values of NO emissions (<10 ppb) across the whole polarisation curve.

  5. Testing visual short-term memory of pigeons (Columba livia) and a rhesus monkey (Macaca mulatta) with a location change detection task.

    Science.gov (United States)

    Leising, Kenneth J; Elmore, L Caitlin; Rivera, Jacquelyne J; Magnotti, John F; Katz, Jeffrey S; Wright, Anthony A

    2013-09-01

    Change detection is commonly used to assess capacity (number of objects) of human visual short-term memory (VSTM). Comparisons with the performance of non-human animals completing similar tasks have shown similarities and differences in object-based VSTM, which is only one aspect ("what") of memory. Another important aspect of memory, which has received less attention, is spatial short-term memory for "where" an object is in space. In this article, we show for the first time that a monkey and pigeons can be accurately trained to identify location changes, much as humans do, in change detection tasks similar to those used to test object capacity of VSTM. The subject's task was to identify (touch/peck) an item that changed location across a brief delay. Both the monkey and pigeons showed transfer to delays longer than the training delay, to greater and smaller distance changes than in training, and to novel colors. These results are the first to demonstrate location-change detection in any non-human species and encourage comparative investigations into the nature of spatial and visual short-term memory.

  6. Capture-based next-generation sequencing reveals multiple actionable mutations in cancer patients failed in traditional testing.

    Science.gov (United States)

    Xie, Jing; Lu, Xiongxiong; Wu, Xue; Lin, Xiaoyi; Zhang, Chao; Huang, Xiaofang; Chang, Zhili; Wang, Xinjing; Wen, Chenlei; Tang, Xiaomei; Shi, Minmin; Zhan, Qian; Chen, Hao; Deng, Xiaxing; Peng, Chenghong; Li, Hongwei; Fang, Yuan; Shao, Yang; Shen, Baiyong

    2016-05-01

    Targeted therapies including monoclonal antibodies and small molecule inhibitors have dramatically changed the treatment of cancer over past 10 years. Their therapeutic advantages are more tumor specific and with less side effects. For precisely tailoring available targeted therapies to each individual or a subset of cancer patients, next-generation sequencing (NGS) has been utilized as a promising diagnosis tool with its advantages of accuracy, sensitivity, and high throughput. We developed and validated a NGS-based cancer genomic diagnosis targeting 115 prognosis and therapeutics relevant genes on multiple specimen including blood, tumor tissue, and body fluid from 10 patients with different cancer types. The sequencing data was then analyzed by the clinical-applicable analytical pipelines developed in house. We have assessed analytical sensitivity, specificity, and accuracy of the NGS-based molecular diagnosis. Also, our developed analytical pipelines were capable of detecting base substitutions, indels, and gene copy number variations (CNVs). For instance, several actionable mutations of EGFR,PIK3CA,TP53, and KRAS have been detected for indicating drug susceptibility and resistance in the cases of lung cancer. Our study has shown that NGS-based molecular diagnosis is more sensitive and comprehensive to detect genomic alterations in cancer, and supports a direct clinical use for guiding targeted therapy.

  7. The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Muslumanoglu, Hamza

    2014-02-01

    Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

  8. Test-retest variability of multifocal electroretinography in normal volunteers and short-term variability in hydroxychloroquine users

    Directory of Open Access Journals (Sweden)

    Browning DJ

    2014-08-01

    Full Text Available David J Browning,1 Chong Lee2 1Charlotte Eye, Ear, Nose and Throat Associates, 2University of North Carolina – Charlotte, Charlotte, NC, USA Purpose: To determine measurement variability of N1P1 amplitudes and the R1/R2 ratio in normal subjects and hydroxychloroquine users without retinopathy. Design: Retrospective, observational study. Subjects: Normal subjects (n=21 and 44 patients taking hydroxychloroquine (n=44 without retinopathy. Methods: Multifocal electroretinography (mfERG was performed twice in one session in the 21 normal subjects and twice within 1 year in the hydroxychloroquine users, during which time no clinical change in macular status occurred. Main outcome measures: N1P1 amplitudes of rings R1–R5, the R1/R2 ratio, and coefficients of repeatability (COR for these measurements. Results: Values for N1P1 amplitudes in hydroxychloroquine users were reduced compared with normal subjects by the known effect of age, but R1/R2 was not affected by age. The COR for R1–R5 ranged from 43% to 52% for normal subjects and from 43% to 59% for hydroxychloroquine users; for R1/R2 the COR was 29% in normal subjects and 45% in hydroxychloroquine users. Conclusion: mfERG measurements show high test-retest variability, limiting the ability of a single mfERG test to influence a decision to stop hydroxychloroquine; corroborative evidence with a different ancillary test is recommended in a suspicious case. Keywords: multifocal electroretinography, hydroxychloroquine, test-retest variability 

  9. Characterization of new eye drops with choline salicylate and assessment of their irritancy by in vitro short time exposure tests

    OpenAIRE

    Wroblewska, Katarzyna; Kucinska, Małgorzata; Murias, Marek; Lulek, Janina

    2015-01-01

    The aim of our study was to examine the irritation potential of new eye drops containing 2% choline salicylate (CS) as an active pharmaceutical ingredient (API) and various polymers increasing eye drop viscosity (hydroxyethylcellulose, hydroxypropyl methylcellulose, methylcellulose, polyvinyl alcohol, polyvinylpyrrolidone). The standard method for assessing the potential of irritating substances has been the Draize rabbit eye test. However the European Centre for Validation of Alternative Met...

  10. An assessment of time involved in pre-test case review and counseling for a whole genome sequencing clinical research program.

    Science.gov (United States)

    Williams, Janet L; Faucett, W Andrew; Smith-Packard, Bethanny; Wagner, Monisa; Williams, Marc S

    2014-08-01

    Whole genome sequencing (WGS) is being used for evaluation of individuals with undiagnosed disease of suspected genetic origin. Implementing WGS into clinical practice will place an increased burden upon care teams with regard to pre-test patient education and counseling about results. To quantitate the time needed for appropriate pre-test evaluation of participants in WGS testing, we documented the time spent by our clinical research group on various activities related to program preparation, participant screening, and consent prior to WGS. Participants were children or young adults with autism, intellectual or developmental disability, and/or congenital anomalies, who have remained undiagnosed despite previous evaluation, and their biologic parents. Results showed that significant time was spent in securing allocation of clinical research space to counsel participants and families, and in acquisition and review of participant's medical records. Pre-enrollment chart review identified two individuals with existing diagnoses resulting in savings of $30,000 for the genome sequencing alone, as well as saving hours of personnel time for genome interpretation and communication of WGS results. New WGS programs should plan for costs associated with additional pre-test administrative planning and patient evaluation time that will be required to provide high quality care.

  11. Short philtrum

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003302.htm Short philtrum To use the sharing features on this page, please enable JavaScript. A short philtrum is a shorter than normal distance between ...

  12. A study on the short-circuit test by fault angle control and the recovery characteristics of the fault current limiter using coated conductor

    International Nuclear Information System (INIS)

    Park, D.K.; Kim, Y.J.; Ahn, M.C.; Yang, S.E.; Seok, B.-Y.; Ko, T.K.

    2007-01-01

    Superconducting fault current limiters (SFCLs) have been developed in many countries, and they are expected to be used in the recent electric power systems, because of their great efficiency for operating these power system stably. It is necessary for resistive FCLs to generate resistance immediately and to have a fast recovery characteristic after the fault clearance, because of re-closing operation. Short-circuit tests are performed to obtained current limiting operational and recovery characteristics of the FCL by a fault controller using a power switching device. The power switching device consists of anti-parallel connected thyristors. The fault occurs at the desired angle by controlling the firing angle of thyristors. Resistive SFCLs have different current limiting characteristics with respect to the fault angle in the first swing during the fault. This study deals with the short-circuit characteristic of FCL coils using two different YBCO coated conductors (CCs), 344 and 344s, by controlling the fault angle and experimental studies on the recovery characteristic by a small current flowing through the SFCL after the fault clearance. Tests are performed at various voltages applied to the SFCL in a saturated liquid nitrogen cooling system

  13. A short-term rating method for heat pump heating systems; phase 5: test of the fault diagnosis systems; Kurztestmethode fuer Waermepumpenanlagen; Phase 5: Test der Fehlerdiagnosesysteme

    Energy Technology Data Exchange (ETDEWEB)

    Zogg, D.; Esfandiar, S.

    2001-07-01

    This final report for the Swiss Federal Office of Energy (SFOE) describes the testing phase of a project that developed systems for the operational monitoring and optimisation of heat pump installations along with a diagnosis system for faults. The heat pump is considered as a sub-system. The report describes two monitoring systems and a simulation model that are used to monitor the state of the heat pump both during commissioning as well as during operation. The aim is also to detect faults as early as possible during the whole of the operational life of the installation. A state-orientated approach is propagated as being cheaper than fixed service intervals or repairing after breakdown and standstill. The development of the two monitoring systems called 'HeatWatch' and 'FuzzyWatch' is described. The effort needed for the parametrisation and training of these systems is discussed. The testing of the systems on two test beds using real-life measured values for a single-family home and further simulation data is described and the results listed. The authors state that the monitoring systems can also be used for refrigeration and air-conditioning systems.

  14. Precision test of many-body QED in the Be$^{+} 2p$ fine structure doublet using short-lived isotopes

    CERN Document Server

    Nörtershäuser, Wilfried; Krieger, Andreas; Pachucki, Krzysztof; Puchalski, Mariusz; Blaum, Klaus; Bissell, Mark L; Frömmgen, Nadja; Hammen, Michael; Kowalska, Magdalena; Krämer, Jörg; Kreim, Kim; Neugart, Rainer; Neyens, Gerda; Sánchez, Rodolfo; Yordanov, Deyan T

    2015-01-01

    Absolute transition frequencies of the $2s\\; ^2{\\rm S}_{1/2} \\rightarrow 2p\\;^2\\mathrm{P}_{1/2,3/2}$ transitions in Be$^+$ were measured for the isotopes $^{7,9-12}$Be. The fine structure splitting of the $2p$ state and its isotope dependence are extracted and compared to results of \\textit{ab initio} calculations using explicitly correlated basis functions, including relativistic and quantum electrodynamics effects at the order of $m \\alpha^6$ and $m \\alpha^7 \\ln \\alpha$. Accuracy has been improved in both the theory and experiment by 2 orders of magnitude, and good agreement is observed. This represents one of the most accurate tests of quantum electrodynamics for many-electron systems, being insensitive to nuclear uncertainties.

  15. Short-term glucagon stimulation test of C-peptide effect on glucose utilization in patients with type 1 diabetes mellitus.

    Science.gov (United States)

    Mojto, Viliam; Rausova, Zuzana; Chrenova, Jana; Dedik, Ladislav

    2015-12-01

    This work aimed to evaluate the use of a four-point glucagon stimulation test of C-peptide effect on glucose utilization in type 1 diabetic patients using a new mathematical model. A group of 32 type 1 diabetic patients and a group of 10 healthy control subjects underwent a four-point glucagon stimulation test with blood sampling at 0, 6, 15 and 30 min after 1 mg glucagon bolus intravenous administration. Pharmacokinetic and pharmacokinetic/pharmacodynamic models of C-peptide effect on glucose utilization versus area under curve (AUC) were used. A two-sample t test and ANOVA with Bonferroni correction were used to test the significance of differences between parameters. A significant difference between control and patient groups regarding the coefficient of whole-body glucose utilization and AUC C-peptide/AUC glucose ratio (p ≪ 0.001 and p = 0.002, respectively) was observed. The high correlation (r = 0.97) between modeled coefficient of whole-body glucose utilization and numerically calculated AUC C-peptide/AUC glucose ratio related to entire cohort indicated the stability of used method. The short-term four-point glucagon stimulation test allows the numerically calculated AUC C-peptide/AUC glucose ratio and/or the coefficient of whole-body glucose utilization calculated from model to be used to diagnostically identify type 1 diabetic patients.

  16. The optimal sequence and selection of screening test items to predict fall risk in older disabled women: the Women's Health and Aging Study.

    Science.gov (United States)

    Lamb, Sarah E; McCabe, Chris; Becker, Clemens; Fried, Linda P; Guralnik, Jack M

    2008-10-01

    Falls are a major cause of disability, dependence, and death in older people. Brief screening algorithms may be helpful in identifying risk and leading to more detailed assessment. Our aim was to determine the most effective sequence of falls screening test items from a wide selection of recommended items including self-report and performance tests, and to compare performance with other published guidelines. Data were from a prospective, age-stratified, cohort study. Participants were 1002 community-dwelling women aged 65 years old or older, experiencing at least some mild disability. Assessments of fall risk factors were conducted in participants' homes. Fall outcomes were collected at 6 monthly intervals. Algorithms were built for prediction of any fall over a 12-month period using tree classification with cross-set validation. Algorithms using performance tests provided the best prediction of fall events, and achieved moderate to strong performance when compared to commonly accepted benchmarks. The items selected by the best performing algorithm were the number of falls in the last year and, in selected subpopulations, frequency of difficulty balancing while walking, a 4 m walking speed test, body mass index, and a test of knee extensor strength. The algorithm performed better than that from the American Geriatric Society/British Geriatric Society/American Academy of Orthopaedic Surgeons and other guidance, although these findings should be treated with caution. Suggestions are made on the type, number, and sequence of tests that could be used to maximize estimation of the probability of falling in older disabled women.

  17. Estimating the short-circuit impedance

    DEFF Research Database (Denmark)

    Nielsen, Arne Hejde; Pedersen, Knud Ole Helgesen; Poulsen, Niels Kjølstad

    1997-01-01

    A method for establishing a complex value of the short-circuit impedance from naturally occurring variations in voltage and current is discussed. It is the symmetrical three phase impedance at the fundamental grid frequency there is looked for. The positive sequence components in voltage...... and current are derived each period, and the short-circuit impedance is estimated from variations in these components created by load changes in the grid. Due to the noisy and dynamic grid with high harmonic distortion it is necessary to threat the calculated values statistical. This is done recursively...... through a RLS-algorithm. The algorithms have been tested and implemented on a PC at a 132 kV substation supplying a rolling mill. Knowing the short-circuit impedance gives the rolling mill an opportunity to adjust the arc furnace operation to keep flicker below a certain level. Therefore, the PC performs...

  18. Short-term carcinogenicity testing of a potent murine intestinal mutagen, 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP), in Apc1638N transgenic mice

    DEFF Research Database (Denmark)

    Sørensen, Ilona Kryspin; Kristiansen, E.; Mortensen, Alicja

    1997-01-01

    others, mammary tumors, We have studied these mice in a short-term carcinogenicity test with 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP), a potent murine small intestinal mutagen and lymphomagen. Upon dietary administration of 0.03% PhIP in a short-term (6 months) study, a significantly...

  19. Study of HIV-1 subtypes in serodiscordant couples attending an integrated counselling and testing centre in Mumbai using heteroduplex mobility analysis and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Mehta P

    2010-01-01

    Full Text Available Aims: To determine the prevalent subtypes of HIV-1 in serodiscordant couples. Setting: Integrated Counselling and Testing Centre (ICTC, Department of Microbiology. Study Design: Prospective pilot study. Participants: Thirty HIV-1 serodiscordant couples. Inclusion Criteria: a Documentation of HIV-1 infection in one partner and seronegative status in the other, current history of continued unprotected sexual activity within the partnership, demonstration that they have been in a partnership for at least 1 year and are not currently on highly active antiretroviral therapy HAART; b willingness of both partners to provide written informed consent including consent to continued couple counselling for 3 months. Materials and Methods: HIV-1 subtyping was carried out by heteroduplex mobility analysis (HMA by amplifying env region; and DNA sequencing by amplifying gag region. Results: HIV-1 env gene was amplified successfully in 10/30 samples; gag gene, in 25/30 samples; and both env and gag gene were amplified successfully in 5/30 samples. HIV-1 subtype C was detected from 21 samples; subtype B, from 7; and subtype A, from 2. Sample from 1 positive partner was detected as subtype C by env HMA and subtype B by gag sequencing. Conclusion: HIV-1 subtype C was found to be the predominant subtype of HIV-1 in serodiscordant couples attending our ICTC, followed by HIV-1 subtype B and HIV-1 subtype A, respectively. DNA sequencing was found to be the most reliable method for determining the subtypes of HIV-1.

  20. Improvement of abnormal vaginal flora in Ugandan women by self-testing and short use of intravaginal antimicrobials.

    Science.gov (United States)

    Donders, G; Bellen, G; Donders, F; Pinget, J; Vandevelde, I; Michiels, T; Byamughisa, J

    2017-04-01

    The vaginal composition of African women is more often lactobacillus-deficient compared to that of women from other areas around the world. Lactobacillus-deficient microflora is a known risk factor for serious health problems, such as preterm birth, cervix cancer, and entrapment of human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs). The aim of this study was to assess the effect of local vaginal antibiotic or antiseptic treatment on abnormal vaginal flora (AVF), aerobic vaginitis (AV), and bacterial vaginosis (BV) among women in rural, semi-urban, and urban areas in Uganda, as compared to placebo. In a double-blind, placebo-controlled, randomized trial, 300 women presenting for outpatient routine, follow-up, or medical care at Mulago Hospital in Kampala, Uganda, were enrolled to receive 6 days of treatment with vaginal rifaximin (RFX), dequalinium chloride (DQC), or placebo if they had an increased vaginal pH of >4.5 as determined by self-testing. At initial visit and at control visit after 4 weeks, a smear was taken for blinded wet mount microscopy to determine AVF, BV, AV, and Candida severity scores. As compared to placebo, both RFX or DQC treatments dramatically diminished BV prevalence and severity from the initial to follow-up visit: the BV score declined from 2.5 to 1.6 (p vaginal microbiome composition of women with disturbed vaginal microflora. As African women have high prevalences of BV, AV, and AVF, this approach could improve their odds to prevent health-compromising complications. Further studies assessing direct health outcomes are needed to substantiate this.

  1. Testing questionnaires “Liebowitz Social Anxiety Scale” and “Fear of Negative Evaluation Scale” (short version

    Directory of Open Access Journals (Sweden)

    Irina V. Grigorieva

    2016-03-01

    Full Text Available Social anxiety has a negative impact on individual’s daily life and disturbs his or hers social adaptation. Socially anxious people are often lonely, have difficulties in meeting new people and communicating with others. Social anxiety can also be a serious obstacle to professional growth and career development, can interfere with obtaining new skills and knowledge. Severe social anxiety is often associated with a variety of disorders, including depression, alcohol and drug addiction, eating disorders. However, social anxiety has a high prevalence among population. In this regard, it is becoming increasingly important to diagnose social anxiety. Therefore, the aim of our study was the validation of two questionnaires measuring social anxiety “Liebowitz Social Anxiety Scale“ and “Fear of Negative Evaluation Scale“. The validation was conducted on 179 people (65 men and 114 women, aged from 18 to 35 years. “Liebowitz Social Anxiety Scale“ measures the degree of anxiety and a tendency to avoidance occurring in various social situations: situations of social interaction and performance situations. «Fear of negative evaluation (brief version» measures the central construct underlying social anxiety - the fear of negative evaluation. As a result of factor analysis of the data it is demonstrated, that “Liebowitz Social Anxiety Scale“ has three-factor structure. Single-factor structure of the «Fear of Negative Evaluation Scale» is confirmed. It is shown that all the subscale “Liebowitz Social Anxiety Scale“ and “Fear of Negative Evaluation Scale (brief version“ has good internal consistency, high test-retest reliability and external validity.

  2. Improvement of human cell line activation test (h-CLAT) using short-time exposure methods for prevention of false-negative results.

    Science.gov (United States)

    Narita, Kazuto; Ishii, Yuuki; Vo, Phuc Thi Hong; Nakagawa, Fumiko; Ogata, Shinichi; Yamashita, Kunihiko; Kojima, Hajime; Itagaki, Hiroshi

    2018-01-01

    Recently, animal testing has been affected by increasing ethical, social, and political concerns regarding animal welfare. Several in vitro safety tests for evaluating skin sensitization, such as the human cell line activation test (h-CLAT), have been proposed. However, similar to other tests, the h-CLAT has produced false-negative results, including in tests for acid anhydride and water-insoluble chemicals. In a previous study, we demonstrated that the cause of false-negative results from phthalic anhydride was hydrolysis by an aqueous vehicle, with IL-8 release from THP-1 cells, and that short-time exposure to liquid paraffin (LP) dispersion medium could reduce false-negative results from acid anhydrides. In the present study, we modified the h-CLAT by applying this exposure method. We found that the modified h-CLAT is a promising method for reducing false-negative results obtained from acid anhydrides and chemicals with octanol-water partition coefficients (LogK ow ) greater than 3.5. Based on the outcomes from the present study, a combination of the original and the modified h-CLAT is suggested for reducing false-negative results. Notably, the combination method provided a sensitivity of 95% (overall chemicals) or 93% (chemicals with LogK ow > 2.0), and an accuracy of 88% (overall chemicals) or 81% (chemicals with LogK ow > 2.0). We found that the combined method is a promising evaluation scheme for reducing false-negative results seen in existing in vitro skin-sensitization tests. In the future, we expect a combination of original and modified h-CLAT to be applied in a newly developed in vitro test for evaluating skin sensitization.

  3. Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.

    Science.gov (United States)

    Alkhateeb, Abedalrhman; Rueda, Luis

    2017-08-01

    Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers. Based on a z-score threshold, Zseq sweeps through the sequences again and filters those with a z-score less than the user-defined threshold. Zseq algorithm is able to provide a better mapping rate; it reduces the number of ambiguous bases significantly in comparison with other methods. Evaluation of the filtered reads has been conducted by aligning the reads and assembling the transcripts using the reference genome as well as de novo assembly. The assembled transcripts show a better discriminative ability to separate cancer and normal samples in comparison with another state-of-the-art method. Moreover, de novo assembled transcripts from the reads filtered by Zseq have longer genomic sequences than other tested methods. Estimating the threshold of the cutoff point is introduced using labeling rules with optimistic results.

  4. Perceptions of randomness in binary sequences: Normative, heuristic, or both?

    Science.gov (United States)

    Reimers, Stian; Donkin, Chris; Le Pelley, Mike E

    2018-03-01

    When people consider a series of random binary events, such as tossing an unbiased coin and recording the sequence of heads (H) and tails (T), they tend to erroneously rate sequences with less internal structure or order (such as HTTHT) as more probable than sequences containing more structure or order (such as HHHHH). This is traditionally explained as a local representativeness effect: Participants assume that the properties of long sequences of random outcomes-such as an equal proportion of heads and tails, and little internal structure-should also apply to short sequences. However, recent theoretical work has noted that the probability of a particular sequence of say, heads and tails of length n, occurring within a larger (>n) sequence of coin flips actually differs by sequence, so P(HHHHH) rational norms based on limited experience. We test these accounts. Participants in Experiment 1 rated the likelihood of occurrence for all possible strings of 4, 5, and 6 observations in a sequence of coin flips. Judgments were better explained by representativeness in alternation rate, relative proportion of heads and tails, and sequence complexity, than by objective probabilities. Experiments 2 and 3 gave similar results using incentivized binary choice procedures. Overall the evidence suggests that participants are not sensitive to variation in objective probabilities of a sub-sequence occurring; they appear to use heuristics based on several distinct forms of representativeness. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

    International Nuclear Information System (INIS)

    Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

    2002-01-01

    The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

  6. USPIO-enhanced 3D-cine self-gated cardiac MRI based on a stack-of-stars golden angle short echo time sequence: Application on mice with acute myocardial infarction.

    Science.gov (United States)

    Trotier, Aurélien J; Castets, Charles R; Lefrançois, William; Ribot, Emeline J; Franconi, Jean-Michel; Thiaudière, Eric; Miraux, Sylvain

    2016-08-01

    To develop and assess a 3D-cine self-gated method for cardiac imaging of murine models. A 3D stack-of-stars (SOS) short echo time (STE) sequence with a navigator echo was performed at 7T on healthy mice (n = 4) and mice with acute myocardial infarction (MI) (n = 4) injected with ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles. In all, 402 spokes were acquired per stack with the incremental or the golden angle method using an angle increment of (360/402)° or 222.48°, respectively. A cylindrical k-space was filled and repeated with a maximum number of repetitions (NR) of 10. 3D cine cardiac images at 156 μm resolution were reconstructed retrospectively and compared for the two methods in terms of contrast-to-noise ratio (CNR). The golden angle images were also reconstructed with NR = 10, 6, and 3, to assess cardiac functional parameters (ejection fraction, EF) on both animal models. The combination of 3D SOS-STE and USPIO injection allowed us to optimize the identification of cardiac peaks on navigator signal and generate high CNR between blood and myocardium (15.3 ± 1.0). The golden angle method resulted in a more homogeneous distribution of the spokes inside a stack (P cine images could be obtained without electrocardiogram or respiratory gating in mice. It allows precise measurement of cardiac functional parameters even on MI mice. J. Magn. Reson. Imaging 2016;44:355-365. © 2016 Wiley Periodicals, Inc.

  7. [Spanish normative studies in a young adult population (NEURONORMA young adults Project): norms for the verbal span, visuospatial span, Letter-Number Sequencing, Trail Making Test and Symbol Digit Modalities Test].

    Science.gov (United States)

    Tamayo, F; Casals-Coll, M; Sánchez-Benavides, G; Quintana, M; Manero, R M; Rognoni, T; Calvo, L; Palomo, R; Aranciva, F; Peña-Casanova, J

    2012-01-01

    Verbal and visuospatial span, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test are frequently used in clinical practice to assess attention, executive functions and memory. In the present study, as part of the Spanish normative studies of NEURONORMA young adults Project, normative data adjusted by age and education are provided for digits, Corsi Block-Tapping Task, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test. The sample consisted of 179 participants from 18 to 49 years old, who were cognitively normal. Tables to convert raw scores to scaled scores are provided. Age and education adjusted scores are provided by applying linear regressions. Education affected scores in most of the attention tests; age was found to be related to the visuospatial span and to speed of visuomotor tracking, and there was no relationship as regards sex. The data obtained will be useful in the clinical evaluation of young Spanish adults. Copyright © 2011 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

  8. Branched Adaptive Testing with a Rasch-Model-Calibrated Test: Analysing Item Presentation's Sequence Effects Using the Rasch-Model-Based LLTM

    Science.gov (United States)

    Kubinger, Klaus D.; Reif, Manuel; Yanagida, Takuya

    2011-01-01

    Item position effects provoke serious problems within adaptive testing. This is because different testees are necessarily presented with the same item at different presentation positions, as a consequence of which comparing their ability parameter estimations in the case of such effects would not at all be fair. In this article, a specific…

  9. Specific MRI quality control: development and production of a multimodal test-object. Assessment of MRI sequences

    International Nuclear Information System (INIS)

    Dedieu, Veronique; Bard, Jean-Jacques; Bonnet, Jacques; Buchheit, Isabelle; Confort-Gouny, Sylviane; Certaines, Jacques de; Lacaze, Brigitte; Vincensini, Dominique; Joffre, Francis

    2007-02-01

    After a first part recalling the operation principle of a MRI imager and the modalities of acquisition of MRI images (base MNR experiment, image quality, technical issues, artefacts and main defects of MRI imagers), this document addresses the different types of quality control in MRI and regulatory issues. The third part presents the characteristics of a multimodal test-object which has been developed, the parameters of the specific quality control, and control procedures

  10. Research, Development and Testing of a Fault-Tolerant FPGA-Based Sequencer for CubeSat Launching Applications

    Science.gov (United States)

    2013-03-01

    is implemented in VHDL with the overall clocking setup and top-level design applied in a modular fashion. As illustrated in Figure 24, the design was...words) This thesis concerns various means of implementing fault tolerance in logic for use in a general payload processor design. The first specific...further evolves to selection of the Actel ProASIC3 series of FPGAs. Initial logic test configurations are implemented on a development kit with analysis

  11. The Short French Internet Addiction Test Adapted to Online Sexual Activities: Validation and Links With Online Sexual Preferences and Addiction Symptoms.

    Science.gov (United States)

    Wéry, Aline; Burnay, Jonathan; Karila, Laurent; Billieux, Joël

    2016-01-01

    The goal of this study was to investigate the psychometric properties of a French version of the short Internet Addiction Test adapted to online sexual activities (s-IAT-sex). The French version of the s-IAT-sex was administered to a sample of 401 men. The participants also completed a questionnaire that screened for sexual addiction (PATHOS). The relationships of s-IAT-sex scores with time spent online for online sexual activities (OSAs) and the types of OSAs favored were also considered. Confirmatory analyses supported a two-factor model of s-IAT-sex, corresponding to the factorial structure found in earlier studies that used the short IAT. The first factor regroups loss of control and time management, whereas the second factor regroups craving and social problems. Internal consistency for each factor was evaluated with Cronbach's α coefficient, resulting in .87 for Factor 1, .76 for Factor 2, and .88 for the global scale. Concurrent validity was supported by relationships with symptoms of sexual addiction, types of OSAs practiced, and time spent online for OSAs. The prevalence of sexual addiction (measured by PATHOS) was 28.1% in the current sample of self-selected male OSA users. The French version of the s-IAT-sex presents good psychometric properties and constitutes a useful tool for researchers and practitioners.

  12. Design development and manufacturing sequence of the European water-cooled Pb-17Li test blanket module

    Energy Technology Data Exchange (ETDEWEB)

    Futterer, M.A.; Bielak, B.; Deffain, J.P.; Giancarli, L.; Li Puma, A.; Salavy, J.F.; Szczepanski, J. [CEA Saclay, Gif-sur-Yvette (France). FDRN/DMT/SERMA; Dellis, C. [CEA Grenoble, DTA-CEREM/SGM, Grenoble (France); Nardi, C. [ENEA Frascati, ERG-FUS-TECN-MEC, Frascati (Italy); Schleisiek, K. [Forschungszentrum Karlsruhe GmbH Technik und Umwelt (Germany). Inst. fuer Reaktorsicherheit

    1998-09-01

    In 1996, the European Community started the development of a water-cooled Pb17Li blanket test module for ITER. First tests are currently scheduled to start with the beginning of the basic performance phase prior to D-T operation. The test module is designed to be a representative for a DEMO breeding blanket and relies on the liquid alloy Pb-17Li as both tritium breeder and neutron multiplier material, and water at PWR pressure and temperature as coolant. The structural material is martensitic steel. The straight, box-like structure of this blanket confines a pool of liquid Pb-17Li which is slowly circulated for ex-situ tritium extraction and lithium adjustment. The box and the Pb-17Li pool are separately cooled, the former with toroido-radial tubes, the latter with a bundle of double-walled U-tubes, equally made of martensitic steel and equipped with a permeation barrier. This paper presents the latest design and three manufacturing schemes with different degrees of technology. Advanced techniques such as solid or powder HIP are proposed to provide design flexibility. With a 3D neutronics analysis, the power and tritium generation were determined. (orig.) 11 refs.

  13. Cell short circuit, preshort signature

    Science.gov (United States)

    Lurie, C.

    1980-01-01

    Short-circuit events observed in ground test simulations of DSCS-3 battery in-orbit operations are analyzed. Voltage signatures appearing in the data preceding the short-circuit event are evaluated. The ground test simulation is briefly described along with performance during reconditioning discharges. Results suggest that a characteristic signature develops prior to a shorting event.

  14. Impact of economic fluctuations on suicide mortality in Canada (1926-2008): Testing the Durkheim, Ginsberg, and Henry and Short theories.

    Science.gov (United States)

    Thibodeau, Lise; Lachaud, James

    2016-01-01

    Three theories have been proposed to explain the relationship between suicide and economic fluctuations, including the Durkheim (nonlinear), Ginsberg (procyclical), and Henry and Short (countercyclical) theories. This study tested the effect of economic fluctuations, measured by unemployment rate, on suicide rates in Canada from 1926 to 2008. Autoregressive integrated moving average time-series models were used. The results showed a significant relationship between suicide and economic fluctuation; this association was positive during the contraction period (1926-1950) and negative in the period of economic expansion (1951-1973). Males and females showed differential effects in the period of moderate unemployment (1974-2008). In addition, the suicide rate of mid-adults (45-64) was most impacted by economic fluctuations. Our study tends to support Durkheim's theory and suggests the need for public health responses in times of economic contraction and expansion.

  15. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  16. Tests to determine the release of short-lived fission products from UO2 fuel operating at linear powers of 45 and 60 kW/m

    International Nuclear Information System (INIS)

    Hastings, I.J.; Hunt, C.E.L.; Lipsett, J.J.; MacDonald, R.D.

    1985-09-01

    Experiments have been carried out using a 'sweep gas' technique to determine the behaviour of short-lived fission products within operating, intact UO 2 fuel elements. The Zircaloy-4-clad elements were 600 mm long and contained fuel of density 10.65 - 10.71 Mg/m 3 . A He-2% H 2 carrier gas swept gaseous or volatile fission products out of the operating fuel element past a gamma spectrometer for measurement. We outline our loop model and give full details of calculational procedures. In tests at linear powers of 45 (FIO-122) and 60 kW/m (FIO-124) to a maximum burnup of 80 MW.h/kg U, the species measured directly at the spectrometer during normal operation were generally the short-lived xenons and kryptons. Iodines were not observed during normal operation. The behaviour of I-133 and I-135 was deduced from the decay of Xe-133 and Xe-135 during reactor shutdowns. Plots of R/B (released/born) against λ (decay constant) or effective λ for all isotopes observed at 45 and 60 kW/m show that a line of slope -0.5, corresponding with diffusion kinetics, is a good fit to the measured xenon and krypton data. The inferred release of iodine fits the same line. From this we can extrapolate to an R/B for I-131 of about 5 x 10 -4 at 45 kW/m, and 3 x 10 -3 at 60 kW/m. Both tests were terminated by defects. Under defect conditions, R/B dependence on λ was about 0.6. I-131 release under defect conditions was 5 Ci and 60 mCi for FIO-122 and FI0-124, respectively. 22 refs

  17. Reliability, Validity, and Minimal Detectable Change of Balance Evaluation Systems Test and Its Short Versions in Older Cancer Survivors: A Pilot Study.

    Science.gov (United States)

    Huang, Min H; Miller, Kara; Smith, Kristin; Fredrickson, Kayle; Shilling, Tracy

    2016-01-01

    .86-2.47 points), and MDC (2.39-6.86 points). The Bland-Altman plot revealed no systematic errors. The scores of BESTest, Mini-BEST, and Brief-BEST were correlated significantly with those of ABC Scale (P test-retest reliability, and excellent concurrent validity with the ABC Scale for community-dwelling cancer survivors aged 55 years and older who had completed cancer treatments for at least 3 months. Future studies are necessary to determine the predictive values for determining fall risks using balance assessment tools in older cancer survivors. Clinicians can utilize the BESTest and its short versions to evaluate balance problems in community-dwelling older cancer survivors and apply the established MDC to assess the intervention outcomes.

  18. Short-term test-retest-reliability of conditioned pain modulation using the cold-heat-pain method in healthy subjects and its correlation to parameters of standardized quantitative sensory testing.

    Science.gov (United States)

    Gehling, Julia; Mainka, Tina; Vollert, Jan; Pogatzki-Zahn, Esther M; Maier, Christoph; Enax-Krumova, Elena K

    2016-08-05

    Conditioned Pain Modulation (CPM) is often used to assess human descending pain inhibition. Nine different studies on the test-retest-reliability of different CPM paradigms have been published, but none of them has investigated the commonly used heat-cold-pain method. The results vary widely and therefore, reliability measures cannot be extrapolated from one CPM paradigm to another. Aim of the present study was to analyse the test-retest-reliability of the common heat-cold-pain method and its correlation to pain thresholds. We tested the short-term test-retest-reliability within 40 ± 19.9 h using a cold-water immersion (10 °C, left hand) as conditioning stimulus (CS) and heat pain (43-49 °C, pain intensity 60 ± 5 on the 101-point numeric rating scale, right forearm) as test stimulus (TS) in 25 healthy right-handed subjects (12females, 31.6 ± 14.1 years). The TS was applied 30s before (TSbefore), during (TSduring) and after (TSafter) the 60s CS. The difference between the pain ratings for TSbefore and TSduring represents the early CPM-effect, between TSbefore and TSafter the late CPM-effect. Quantitative sensory testing (QST, DFNS protocol) was performed on both sessions before the CPM assessment. paired t-tests, Intraclass correlation coefficient (ICC), standard error of measurement (SEM), smallest real difference (SRD), Pearson's correlation, Bland-Altman analysis, significance level p Pain ratings during CPM correlated significantly (ICC: 0.411…0.962) between both days, though ratings for TSafter were lower on day 2 (p pain thresholds. The short-term test-retest-reliability of the early CPM-effect using the heat-cold-pain method in healthy subjects achieved satisfying results in terms of the ICC. The SRD of the early CPM effect showed that an individual change of > 20 NRS can be attributed to a real change rather than chance. The late CPM-effect was weaker and not reliable.

  19. Short-term delayed recall of auditory verbal learning test is equivalent to long-term delayed recall for identifying amnestic mild cognitive impairment.

    Directory of Open Access Journals (Sweden)

    Qianhua Zhao

    Full Text Available Delayed recall of words in a verbal learning test is a sensitive measure for the diagnosis of amnestic mild cognitive impairment (aMCI and early Alzheimer's disease (AD. The relative validity of different retention intervals of delayed recall has not been well characterized. Using the Auditory Verbal Learning Test-Huashan version, we compared the differentiating value of short-term delayed recall (AVL-SR, that is, a 3- to 5-minute delay time and long-term delayed recall (AVL-LR, that is, a 20-minute delay time in distinguishing patients with aMCI (n = 897 and mild AD (n = 530 from the healthy elderly (n = 1215. In patients with aMCI, the correlation between AVL-SR and AVL-LR was very high (r = 0.94, and the difference between the two indicators was less than 0.5 points. There was no difference between AVL-SR and AVL-LR in the frequency of zero scores. In the receiver operating characteristic curves analysis, although the area under the curve (AUC of AVL-SR and AVL-LR for diagnosing aMCI was significantly different, the cut-off scores of the two indicators were identical. In the subgroup of ages 80 to 89, the AUC of the two indicators showed no significant difference. Therefore, we concluded that AVL-SR could substitute for AVL-LR in identifying aMCI, especially for the oldest patients.

  20. Evolution of short cognitive test performance in stroke patients with vascular cognitive impairment and vascular dementia: Baseline evaluation and follow-up

    Science.gov (United States)

    Custodio, Nilton; Montesinos, Rosa; Lira, David; Herrera-Perez, Eder; Bardales, Yadira; Valeriano-Lorenzo, Lucia

    2017-01-01

    ABSTRACT. There is limited evidence about the progression of cognitive performance during the post-stroke stage. Objective: To assess the evolution of cognitive performance in stroke patients without vascular cognitive impairment (VCI), patients with vascular mild cognitive impairment (MCI), and patients with vascular dementia (VD). Methods: A prospective cohort of stroke outpatients from two secondary medical centers in Lima, Peru was studied. We performed standardized evaluations at definitive diagnosis (baseline evaluation), and control follow-ups at 6 and 12 months, including a battery of short cognitive tests: Clinical Dementia Rating (CDR), Addenbrooke's Cognitive Examination (ACE), and INECO Frontal Screening (IFS). Results: 152 outpatients completed the follow-up, showing progressive increase in mean score on the CDR(0.34 to 0.46), contrary to the pattern observed on the ACE and IFS (78.18 to 76.48 and 23.63 to 22.24). The box plot for the CDR test showed that VCI patients had progressive worsening (0.79 to 0.16). Conversely, this trend was not observed in subjects without VCI. The box plot for the ACE and IFS showed that, for the majority of the differentiated stroke types, both non-VCI and VCI patients had progressive worsening. Conclusion: According to both ACE and IFS results during a 1-year follow-up, the cognitive performance of stroke patients worsened, a trend which was particularly consistent in infarction-type stroke patients. PMID:29354218

  1. Evolution of short cognitive test performance in stroke patients with vascular cognitive impairment and vascular dementia: Baseline evaluation and follow-up

    Directory of Open Access Journals (Sweden)

    Nilton Custodio

    Full Text Available ABSTRACT. There is limited evidence about the progression of cognitive performance during the post-stroke stage. Objective: To assess the evolution of cognitive performance in stroke patients without vascular cognitive impairment (VCI, patients with vascular mild cognitive impairment (MCI, and patients with vascular dementia (VD. Methods: A prospective cohort of stroke outpatients from two secondary medical centers in Lima, Peru was studied. We performed standardized evaluations at definitive diagnosis (baseline evaluation, and control follow-ups at 6 and 12 months, including a battery of short cognitive tests: Clinical Dementia Rating (CDR, Addenbrooke's Cognitive Examination (ACE, and INECO Frontal Screening (IFS. Results: 152 outpatients completed the follow-up, showing progressive increase in mean score on the CDR(0.34 to 0.46, contrary to the pattern observed on the ACE and IFS (78.18 to 76.48 and 23.63 to 22.24. The box plot for the CDR test showed that VCI patients had progressive worsening (0.79 to 0.16. Conversely, this trend was not observed in subjects without VCI. The box plot for the ACE and IFS showed that, for the majority of the differentiated stroke types, both non-VCI and VCI patients had progressive worsening. Conclusion: According to both ACE and IFS results during a 1-year follow-up, the cognitive performance of stroke patients worsened, a trend which was particularly consistent in infarction-type stroke patients.

  2. Field test of short-notice random inspections for inventory-change verification at a low-enriched-uranium fuel-fabrication plant: Preliminary summary

    International Nuclear Information System (INIS)

    Fishbone, L.G.; Moussalli, G.; Naegele, G.; Ikonomou, P.; Hosoya, M.; Scott, P.; Fager, J.; Sanders, C.; Colwell, D.; Joyner, C.J.

    1994-01-01

    An approach of short-notice random inspections (SNRIs) for inventory-change verification can enhance the effectiveness and efficiency of international safeguards at natural or low-enriched uranium (LEU) fuel fabrication plants. According to this approach, the plant operator declares the contents of nuclear material items before knowing if an inspection will occur to verify them. Additionally, items about which declarations are newly made should remain available for verification for an agreed time. This report details a six-month field test of the feasibility of such SNRIs which took place at the Westinghouse Electric Corporation Commercial Nuclear Fuel Division. Westinghouse personnel made daily declarations about both feed and product items, uranium hexafluoride cylinders and finished fuel assemblies, using a custom-designed computer ''mailbox''. Safeguards inspectors from the IAEA conducted eight SNRIs to verify these declarations. Items from both strata were verified during the SNRIs by means of nondestructive assay equipment. The field test demonstrated the feasibility and practicality of key elements of the SNRI approach for a large LEU fuel fabrication plant

  3. Development and validation testing of a short nutrition questionnaire to identify dietary risk factors in preschoolers aged 12–36 months

    Directory of Open Access Journals (Sweden)

    Niamh Rice

    2015-06-01

    Full Text Available Background: Although imbalances in dietary intakes can have short and longer term influences on the health of preschool children, few tools exist to quickly and easily identify nutritional risk in otherwise healthy young children. Objectives: To develop and test the validity of a parent-administered questionnaire (NutricheQ as a means of evaluating dietary risk in young children (12–36 months. Design: Following a comprehensive development process and internal reliability assessment, the NutricheQ questionnaire was validated in a cohort of 371 Irish preschool children as part of the National Preschool Nutrition Survey. Dietary risk was rated on a scale ranging from 0 to 22 from 11 questions, with a higher score indicating higher risk. Results: Children with higher NutricheQ scores had significantly (p<0.05 lower mean daily intakes of key nutrients such as iron, zinc, vitamin D, riboflavin, niacin, folate, phosphorous, potassium, carotene, retinol, and dietary fibre. They also had lower (p<0.05 intakes of vegetables, fish and fish dishes, meat and infant/toddler milks and higher intakes of processed foods and non-milk beverages, confectionery, sugars and savoury snack foods indicative of poorer dietary quality. Areas under the curve values of 84.7 and 75.6% were achieved for ‘medium’ and ‘high’ dietary risk when compared with expert risk ratings indicating good consistency between the two methods. Conclusion: NutricheQ is a valid method of quickly assessing dietary quality in preschoolers and in identifying those at increased nutritional risk.In ContextAnalysis of data from national food and nutrition surveys typically identifies shortfalls in dietary intakes or quality of young children. This can relate to intakes of micronutrients such as iron or vitamin D as well as to the balance of macronutrients they consume (e.g. fat or sugar. Alongside this lie concerns regarding overweight and obesity and physical inactivity. This combination of

  4. Graph Theoretical Analysis of Functional Brain Networks: Test-Retest Evaluation on Short- and Long-Term Resting-State Functional MRI Data

    Science.gov (United States)

    Wang, Jin-Hui; Zuo, Xi-Nian; Gohel, Suril; Milham, Michael P.; Biswal, Bharat B.; He, Yong

    2011-01-01

    Graph-based computational network analysis has proven a powerful tool to quantitatively characterize functional architectures of the brain. However, the test-retest (TRT) reliability of graph metrics of functional networks has not been systematically examined. Here, we investigated TRT reliability of topological metrics of functional brain networks derived from resting-state functional magnetic resonance imaging data. Specifically, we evaluated both short-term (5 months apart) TRT reliability for 12 global and 6 local nodal network metrics. We found that reliability of global network metrics was overall low, threshold-sensitive and dependent on several factors of scanning time interval (TI, long-term>short-term), network membership (NM, networks excluding negative correlations>networks including negative correlations) and network type (NT, binarized networks>weighted networks). The dependence was modulated by another factor of node definition (ND) strategy. The local nodal reliability exhibited large variability across nodal metrics and a spatially heterogeneous distribution. Nodal degree was the most reliable metric and varied the least across the factors above. Hub regions in association and limbic/paralimbic cortices showed moderate TRT reliability. Importantly, nodal reliability was robust to above-mentioned four factors. Simulation analysis revealed that global network metrics were extremely sensitive (but varying degrees) to noise in functional connectivity and weighted networks generated numerically more reliable results in compared with binarized networks. For nodal network metrics, they showed high resistance to noise in functional connectivity and no NT related differences were found in the resistance. These findings provide important implications on how to choose reliable analytical schemes and network metrics of interest. PMID:21818285

  5. Short communication

    African Journals Online (AJOL)

    abp

    2017-02-01

    Feb 1, 2017 ... which no bacterial cause had been found by culture or by molecular biology. Isolation of ... Germany for sequencing. Analysis with the Blast .... Alain Farra was the principal investigator, working from levies on sites, cultivation ...

  6. Short Communication

    African Journals Online (AJOL)

    huis

    SNP was screened by comparing sequences of PCR products, and the ... A sharp rise in plasma PRL level may induce incubation behaviour and thus terminate ... Therefore, PRL exhibits similar changing profiles in the reproduction cycle and.

  7. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  8. Short communication

    African Journals Online (AJOL)

    abp

    2017-09-04

    Sep 4, 2017 ... Face-to-face interviews were conducted using a standardized ... Short communication. Open Access ... clinic during the time of the study and were invited to participate in the study. .... consume them. This is another ...

  9. SHORT COMMUNICATION

    African Journals Online (AJOL)

    PROF P.T. KAYE

    . SHORT COMMUNICATION. Formation and Structural Analysis of Novel Dibornyl Ethers. Perry T. Kaye*, Andrew R. Duggan, Joseph M. Matjila, Warner E. Molema, and. Swarnam S. Ravindran. Department of Chemistry, Rhodes University, Grahamstown, ...

  10. Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

    Science.gov (United States)

    Biedrzycka, Aleksandra; Sebastian, Alvaro; Migalska, Magdalena; Westerdahl, Helena; Radwan, Jacek

    2017-07-01

    Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage. © 2016 John Wiley & Sons Ltd.

  11. Brain histamine depletion enhances the behavioural sequences complexity of mice tested in the open-field: Partial reversal effect of the dopamine D2/D3 antagonist sulpiride.

    Science.gov (United States)

    Santangelo, Andrea; Provensi, Gustavo; Costa, Alessia; Blandina, Patrizio; Ricca, Valdo; Crescimanno, Giuseppe; Casarrubea, Maurizio; Passani, M Beatrice

    2017-02-01

    Markers of histaminergic dysregulation were found in several neuropsychiatric disorders characterized by repetitive behaviours, thoughts and stereotypies. We analysed the effect of acute histamine depletion by means of i. c.v. injections of alpha-fluoromethylhistidine, a blocker of histidine decarboxylase, on the temporal organization of motor sequences of CD1 mice behaviour in the open-field test. An ethogram encompassing 9 behavioural components was employed. Durations and frequencies were only slightly affected by treatments. However, as revealed by multivariate t-pattern analysis, histamine depletion was associated with a striking increase in the number of behavioural patterns. We found 42 patterns of different composition occurring, on average, 520.90 ± 50.23 times per mouse in the histamine depleted (HD) group, whereas controls showed 12 different patterns occurring on average 223.30 ± 20.64 times. Exploratory and grooming behaviours clustered separately, and the increased pattern complexity involved exclusively exploratory patterns. To test the hypothesis of a histamine-dopamine interplay on behavioural pattern phenotype, non-sedative doses of the D2/D3 antagonist sulpiride (12.5-25-50 mg/kg) were additionally administered to different groups of HD mice. Sulpiride counterbalanced the enhancement of exploratory patterns of different composition, but it did not affect the mean number of patterns at none of the doses used. Our results provide new insights on the role of histamine on repetitive behavioural sequences of freely moving mice. Histamine deficiency is correlated with a general enhancement of pattern complexity. This study supports a putative involvement of histamine in the pathophysiology of tics and related disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Long-Term and Short-Term Effects of Hemodialysis on Liver Function Evaluated Using the Galactose Single-Point Test

    Directory of Open Access Journals (Sweden)

    Yi-Chou Hou

    2014-01-01

    Full Text Available Aim. The galactose single-point (GSP test assesses functioning liver mass by measuring the galactose concentration in the blood 1 hour after its administration. The purpose of this study was to investigate the impact of hemodialysis (HD on short-term and long-term liver function by use of GSP test. Methods. Seventy-four patients on maintenance HD (46 males and 28 females, 60.38 ± 11.86 years with a mean time on HD of 60.77 ± 48.31 months were studied. The GSP values were compared in two groups: (1 before and after single session HD, and (2 after one year of maintenance HD. Results. Among the 74 HD patient, only the post-HD Cr levels and years on dialysis were significantly correlated with GSP values (r=0.280, P<0.05 and r=-0.240, P<0.05, resp.. 14 of 74 patients were selected for GSP evaluation before and after a single HD session, and the hepatic clearance of galactose was similar (pre-HD 410 ± 254 g/mL, post-HD 439 ± 298 g/mL, P=0.49. GSP values decreased from 420.20 ± 175.26 g/mL to 383.40 ± 153.97 g/mL after 1 year maintenance HD in other 15 patients (mean difference: 19.00 ± 37.66 g/mL, P<0.05. Conclusions. Patients on maintenance HD for several years may experience improvement of their liver function. However, a single HD session does not affect liver function significantly as assessed by the GSP test. Since the metabolism of galactose is dependent on liver blood flow and hepatic functional mass, further studies are needed.

  13. Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey.

    Science.gov (United States)

    Tagliani, Elisa; Hassan, Mohamed Osman; Waberi, Yacine; De Filippo, Maria Rosaria; Falzon, Dennis; Dean, Anna; Zignol, Matteo; Supply, Philip; Abdoulkader, Mohamed Ali; Hassangue, Hawa; Cirillo, Daniela Maria

    2017-12-15

    Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.

  14. Investigation on the Short-Circuit Behavior of an Aged IGBT Module Through a 6 kA/1.1 kV Non-Destructive Testing Equipment

    DEFF Research Database (Denmark)

    Wu, Rui; Smirnova, Liudmila; Iannuzzo, Francesco

    2014-01-01

    This paper describes the design and development of a 6 kA/1.1 kV non-destructive testing system, which aims for short circuit testing of high-power IGBT modules. An ultralow stray inductance of 37 nH is achieved in the implementation of the tester. An 100 MHz FPGA supervising unit enables 10 ns...

  15. Optimal planning of series resistor to control time constant of test circuit for high-voltage AC circuit-breakers

    OpenAIRE

    Yoon-Ho Kim; Jung-Hyeon Ryu; Jin-Hwan Kim; Kern-Joong Kim

    2016-01-01

    The equivalent test circuit that can deliver both short-circuit current and recovery voltage is used to verify the performance of high-voltage circuit breakers. Most of the parameters in this circuit can be obtained by using a simple calculation or a simulation program. The ratings of the circuit breaker include rated short-circuit breaking current, rated short-circuit making current, rated operating sequence of the circuit breaker and rated short-time current. Among these ratings, the short-...

  16. Idiopathic short stature

    Directory of Open Access Journals (Sweden)

    Vlaški Jovan

    2013-01-01

    Full Text Available Growth is a complex process and the basic characteristic of child- hood growth monitoring provides insight into the physiological and pathological events in the body. Statistically, the short stature means departure from the values of height for age and sex (in a particular environment, which is below -2 standard deviation score, or less than -2 standard deviation, i.e. below the third percentile. Advances in molecular genetics have contributed to the improvement of diagnostics in endocrinology. Analysis of patients’ genotypes should not be performed before taking a classical history, detailed clinical examination and appropriate tests. In patients with idiopathic short stature specific causes are excluded, such as growth hormone deficiency, Turner syndrome, short stature due to low birth weight, intrauterine growth retardation, small for gestational age, dysmorphology syndromes and chronic childhood diseases. The exclusion of abovementioned conditions leaves a large number of children with short stature whose etiology includes patients with genetic short stature or familial short stature and those who are low in relation to genetic potential, and who could also have some unrecognized endocrine defect. Idiopathic short stature represents a short stature of unknown cause of heterogeneous etiology, and is characterized by a normal response of growth hormone during stimulation tests (>10 ng/ml or 20 mJ/l, without other disorders, of normal body mass and length at birth. In idiopathic short stature standard deviation score rates <-2.25 (-2 to -3 or <1.2 percentile. These are also criteria for the initiation of growth hormone therapy. In children with short stature there is also the presence of psychological and social suffering. Goals of treatment with growth hormone involve achieving normal height and normal growth rate during childhood.

  17. Idiographic duo-trio tests using a constant-reference based on preference of each consumer: Sample presentation sequence in difference test can be customized for individual consumers to reduce error.

    Science.gov (United States)

    Kim, Min-A; Sim, Hye-Min; Lee, Hye-Seong

    2016-11-01

    As reformulations and processing changes are increasingly needed in the food industry to produce healthier, more sustainable, and cost effective products while maintaining superior quality, reliable measurements of consumers' sensory perception and discrimination are becoming more critical. Consumer discrimination methods using a preferred-reference duo-trio test design have been shown to be effective in improving the discrimination performance by customizing sample presentation sequences. However, this design can add complexity to the discrimination task for some consumers, resulting in more errors in sensory discrimination. The objective of the present study was to investigate the effects of different types of test instructions using the preference-reference duo-trio test design where a paired-preference test is followed by 6 repeated preferred-reference duo-trio tests, in comparison to the analytical method using the balanced-reference duo-trio. Analyses of d' estimates (product-related measure) and probabilistic sensory discriminators in momentary numbers of subjects showing statistical significance (subject-related measure) revealed that only preferred-reference duo-trio test using affective reference-framing, either by providing no information about the reference or information on a previously preferred sample, improved the sensory discrimination more than the analytical method. No decrease in discrimination performance was observed with any type of instruction, confirming that consumers could handle the test methods. These results suggest that when repeated tests are feasible, using the affective discrimination method would be operationally more efficient as well as ecologically more reliable for measuring consumers' sensory discrimination ability. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  19. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  20. Electrothermal Action of the Pulse of the Current of a Short Artificial-Lightning Stroke on Test Specimens of Wires and Cables of Electric Power Objects

    Science.gov (United States)

    Baranov, M. I.; Rudakov, S. V.

    2018-03-01

    The authors have given results of investigations of the electrothermal action of aperiodic pulses of temporal shape 10/350 μs of the current of a short artificial-lightning stroke on test specimens of electric wires and cables with copper and aluminum cores and sheaths with polyvinylchloride and polyethylene insulations of power circuits of industrial electric power objects. It has been shown that the thermal stability of such wires and cables is determined by the action integral of the indicated current pulse. The authors have found the maximum permissible and critical densities of this pulse in copper and aluminum current-carrying parts of the wires and cables. High-current experiments conducted under high-voltage laboratory conditions on a unique generator of 10/350 μs pulses of an artificial-lightning current with amplitude-time parameters normalized according to the existing requirements of international and national standards and with tolerances on them have confirmed the reliability of the proposed calculated estimate for thermal lightning resistance of cabling and wiring products.

  1. Finite strain anisotropic elasto-plastic model for the simulation of the forming and testing of metal/short fiber reinforced polymer clinch joints at room temperature

    Science.gov (United States)

    Dean, A.; Rolfes, R.; Behrens, A.; Bouguecha, A.; Hübner, S.; Bonk, C.; Grbic, N.

    2017-10-01

    There is a strong trend in the automotive industry to reduce car body-, chassis- and power-train mass in order to lower carbon emissions. More wide spread use of lightweight short fiber reinforced polymer (SFRP) is a promising approach to attain this goal. This poses the challenge of how to integrate new SFRP components by joining them to traditional sheet metal structures. Recently (1), the clinching technique has been successfully applied as a suitable joining method for dissimilar material such as SFRP and Aluminum. The material pairing PA6GF30 and EN AW 5754 is chosen for this purpose due to their common application in industry. The current contribution presents a verification and validation of a finite strain anisotropic material model for SFRP developed in (2) for the FE simulation of the hybrid clinching process. The finite fiber rotation during forming and separation, and thus the change of the preferential material direction, is represented in this model. Plastic deformations in SFRP are considered in this model via an invariant based non-associated plasticity formulation following the multiplicative decomposition approach of the deformation gradient where the stress-free intermediate configuration is introduced. The model allows for six independent characterization curves. The aforementioned material model allows for a detailed simulation of the forming process as well as a simulative prediction of the shear test strength of the produced joint at room temperature.

  2. Electrothermal Action of the Pulse of the Current of a Short Artificial-Lightning Stroke on Test Specimens of Wires and Cables of Electric Power Objects

    Science.gov (United States)

    Baranov, M. I.; Rudakov, S. V.

    2018-05-01

    The authors have given results of investigations of the electrothermal action of aperiodic pulses of temporal shape 10/350 μs of the current of a short artificial-lightning stroke on test specimens of electric wires and cables with copper and aluminum cores and sheaths with polyvinylchloride and polyethylene insulations of power circuits of industrial electric power objects. It has been shown that the thermal stability of such wires and cables is determined by the action integral of the indicated current pulse. The authors have found the maximum permissible and critical densities of this pulse in copper and aluminum current-carrying parts of the wires and cables. High-current experiments conducted under high-voltage laboratory conditions on a unique generator of 10/350 μs pulses of an artificial-lightning current with amplitude-time parameters normalized according to the existing requirements of international and national standards and with tolerances on them have confirmed the reliability of the proposed calculated estimate for thermal lightning resistance of cabling and wiring products.

  3. Field test of short-notice random inspections for inventory-change verification at a low-enriched-uranium fuel-fabrication plant

    International Nuclear Information System (INIS)

    Fishbone, L.G.; Moussalli, G.; Naegele, G.

    1995-01-01

    An approach of short-notice random inspections (SNRIs) for inventory-change verification can enhance the effectiveness and efficiency of international safeguards at natural or low-enriched uranium (LEU) fuel fabrication plants. According to this approach, the plant operator declares the contents of nuclear material items before knowing if an inspection will occur to verify them. Additionally, items about which declarations are newly made should remain available for verification for an agreed time. Then a statistical inference can be made from verification results for items verified during SNRIs to the entire populations, i.e. the entire strata, even if inspectors were not present when many items were received or produced. A six-month field test of the feasibility of such SNRIs took place at the Westinghouse Electric Corporation Commercial Nuclear Fuel Division during 1993. Westinghouse personnel made daily declarations about both feed and product items, uranium hexafluoride cylinders and finished fuel assemblies, using a custom-designed computer ''mailbox''. Safeguards inspectors from the IAEA conducted eight SNRIs to verify these declarations. They arrived unannounced at the plant, in most cases immediately after travel from Canada, where the IAEA maintains a regional office. Items from both strata were verified during the SNRIs by meant of nondestructive assay equipment

  4. Short Stature

    DEFF Research Database (Denmark)

    Christesen, Henrik Boye Thybo; Pedersen, Birgitte Tønnes; Pournara, Effie

    2016-01-01

    -scale, non-interventional, multinational study. The patient cohort consisted of 5996 short pediatric patients diagnosed with growth hormone deficiency (GHD), Turner syndrome (TS) or born small for gestational age (SGA). The proportions of children with baseline height standard deviation score (SDS) below......The use of appropriate growth standards/references is of significant clinical importance in assessing the height of children with short stature as it may determine eligibility for appropriate therapy. The aim of this study was to determine the impact of using World Health Organization (WHO) instead...... of national growth standards/references on height assessment in short children. Data were collected from routine clinical practice (1998-2014) from nine European countries that have available national growth references and were enrolled in NordiNet® International Outcome Study (IOS) (NCT00960128), a large...

  5. Assessing hydraulic connections across a complex sequence of volcanic rocks - Analysis of U-20 WW multiple-well aquifer test, Pahute Mesa, Nevada National Security Site, Nevada

    Science.gov (United States)

    Garcia, C. Amanda; Fenelon, Joseph M.; Halford, Keith J.; Reiner, Steven R.; Laczniak, Randell J.

    2011-01-01

    Groundwater beneath Pahute Mesa flows through a complexly layered sequence of volcanic rock aquifers and confining units that have been faulted into distinct structural blocks. Hydraulic property estimates of rocks and structures in this flow system are necessary to assess radionuclide migration near underground nuclear testing areas. The U.S. Geological Survey (USGS) used a 12 month (October 1, 2008— October 1, 2009) intermittent pumping schedule of well U-20 WW and continuously monitored water levels in observation wells ER-20-6 #3, UE-20bh 1, and U-20bg as a multi-well aquifer test to evaluate hydraulic connections across structural blocks, bulk hydraulic properties of volcanic rocks, and the hydraulic significance of a major fault. Measured water levels were approximated using synthetic water levels generated from an analytical model. Synthetic water levels are a summation of environmental water-level fluctuations and a Theis (1935) transform of the pumping signal from flow rate to water-level change. Drawdown was estimated by summing residual differences between measured and synthetic water levels and the Theis-transformed pumping signal from April to September 2009. Drawdown estimates were used in a three‑dimensional numerical model to estimate hydraulic properties of distinct aquifers, confining units, and a major fault.

  6. Nucleic Acid Amplification Testing and Sequencing Combined with Acid-Fast Staining in Needle Biopsy Lung Tissues for the Diagnosis of Smear-Negative Pulmonary Tuberculosis.

    Science.gov (United States)

    Jiang, Faming; Huang, Weiwei; Wang, Ye; Tian, Panwen; Chen, Xuerong; Liang, Zongan

    2016-01-01

    Smear-negative pulmonary tuberculosis (PTB) is common and difficult to diagnose. In this study, we investigated the diagnostic value of nucleic acid amplification testing and sequencing combined with acid-fast bacteria (AFB) staining of needle biopsy lung tissues for patients with suspected smear-negative PTB. Patients with suspected smear-negative PTB who underwent percutaneous transthoracic needle biopsy between May 1, 2012, and June 30, 2015, were enrolled in this retrospective study. Patients with AFB in sputum smears were excluded. All lung biopsy specimens were fixed in formalin, embedded in paraffin, and subjected to acid-fast staining and tuberculous polymerase chain reaction (TB-PCR). For patients with positive AFB and negative TB-PCR results in lung tissues, probe assays and 16S rRNA sequencing were used for identification of nontuberculous mycobacteria (NTM). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy of PCR and AFB staining were calculated separately and in combination. Among the 220 eligible patients, 133 were diagnosed with TB (men/women: 76/57; age range: 17-80 years, confirmed TB: 9, probable TB: 124). Forty-eight patients who were diagnosed with other specific diseases were assigned as negative controls, and 39 patients with indeterminate final diagnosis were excluded from statistical analysis. The sensitivity, specificity, PPV, NPV, and accuracy of histological AFB (HAFB) for the diagnosis of smear-negative were 61.7% (82/133), 100% (48/48), 100% (82/82), 48.5% (48/181), and 71.8% (130/181), respectively. The sensitivity, specificity, PPV, and NPV of histological PCR were 89.5% (119/133), 95.8% (46/48), 98.3% (119/121), and 76.7% (46/60), respectively, demonstrating that histological PCR had significantly higher accuracy (91.2% [165/181]) than histological acid-fast staining (71.8% [130/181]), P pulmonary tuberculosis. For patients with positive histological AFB and

  7. Lithofacies and sequence stratigraphic description of the upper part of the Avon Park Formation and the Arcadia Formation in U.S. Geological Survey G–2984 test corehole, Broward County, Florida

    Science.gov (United States)

    Cunningham, Kevin J.; Robinson, Edward

    2017-07-18

    Rock core and sediment from U.S. Geological Survey test corehole G–2984 completed in 2011 in Broward County, Florida, provide an opportunity to improve the understanding of the lithostratigraphic, sequence stratigraphic, and hydrogeologic framework of the intermediate confining unit and Floridan aquifer system in southeastern Florida. A multidisciplinary approach including characterization of sequence stratigraphy, lithofacies, ichnology, foraminiferal paleontology, depositional environments, porosity, and permeability was used to describe the geologic samples from this test corehole. This information has produced a detailed characterization of the lithofacies and sequence stratigraphy of the upper part of the middle Eocene Avon Park Formation and Oligocene to middle Miocene Arcadia Formation. This enhancement of the knowledge of the sequence stratigraphic framework is especially important, because subaerial karst unconformities at the upper boundary of depositional cycles at various hierarchical scales are commonly associated with secondary porosity and enhanced permeability in the Floridan aquifer system.

  8. Proband-only medical exome sequencing as a cost-effective first-tier genetic diagnostic test for patients without prior molecular tests and clinical diagnosis in a developing country: the China experience.

    Science.gov (United States)

    Hu, Xuyun; Li, Niu; Xu, Yufei; Li, Guoqiang; Yu, Tingting; Yao, Ru-En; Fu, Lijun; Wang, Jiwen; Yin, Lei; Yin, Yong; Wang, Ying; Jin, Xingming; Wang, Xiumin; Wang, Jian; Shen, Yiping

    2017-11-02

    PurposeTo evaluate the performance of proband-only medical exome sequencing (POMES) as a cost-effective first-tier diagnostic test for pediatric patients with unselected conditions.MethodsA total of 1,323 patients were tested by POMES, which targeted 2,742 known disease-causing genes. Clinical relevant variants were Sanger-confirmed in probands and parents. We assessed the diagnostic validity and clinical utility of POMES by means of a survey questionnaire.ResultsPOMES, ordered by 136 physicians, identified 512 pathogenic or likely pathogenic variants associated with over 200 conditions. The overall diagnostic rate was 28.8%, ranging from 10% in neonatal intensive care unit patients to over 35% in pediatric intensive care unit patients. The test results had an impact on the management of the 45.1% of patients for whom there were positive findings. The average turnaround time was 57 days; the cost was $360/case.ConclusionWe adopted a relatively efficient and cost-effective approach in China for the molecular diagnosis of pediatric patients with suspected genetic conditions. While training for clinical geneticists and other specialists is lagging behind in China POMES is serving as a diagnostic equalizer for patients who do not normally receive extensive clinical evaluation and clinical diagnosis prior to testing. This Chinese experience should be applicable to other developing countries that are lacking clinical, financial, and personnel resources.GENETICS in MEDICINE advance online publication, 2 November 2017; doi:10.1038/gim.2017.195.

  9. Nucleic Acid Amplification Testing and Sequencing Combined with Acid-Fast Staining in Needle Biopsy Lung Tissues for the Diagnosis of Smear-Negative Pulmonary Tuberculosis.

    Directory of Open Access Journals (Sweden)

    Faming Jiang

    Full Text Available Smear-negative pulmonary tuberculosis (PTB is common and difficult to diagnose. In this study, we investigated the diagnostic value of nucleic acid amplification testing and sequencing combined with acid-fast bacteria (AFB staining of needle biopsy lung tissues for patients with suspected smear-negative PTB.Patients with suspected smear-negative PTB who underwent percutaneous transthoracic needle biopsy between May 1, 2012, and June 30, 2015, were enrolled in this retrospective study. Patients with AFB in sputum smears were excluded. All lung biopsy specimens were fixed in formalin, embedded in paraffin, and subjected to acid-fast staining and tuberculous polymerase chain reaction (TB-PCR. For patients with positive AFB and negative TB-PCR results in lung tissues, probe assays and 16S rRNA sequencing were used for identification of nontuberculous mycobacteria (NTM. The sensitivity, specificity, positive predictive value (PPV, negative predictive value (NPV, and diagnostic accuracy of PCR and AFB staining were calculated separately and in combination.Among the 220 eligible patients, 133 were diagnosed with TB (men/women: 76/57; age range: 17-80 years, confirmed TB: 9, probable TB: 124. Forty-eight patients who were diagnosed with other specific diseases were assigned as negative controls, and 39 patients with indeterminate final diagnosis were excluded from statistical analysis. The sensitivity, specificity, PPV, NPV, and accuracy of histological AFB (HAFB for the diagnosis of smear-negative were 61.7% (82/133, 100% (48/48, 100% (82/82, 48.5% (48/181, and 71.8% (130/181, respectively. The sensitivity, specificity, PPV, and NPV of histological PCR were 89.5% (119/133, 95.8% (46/48, 98.3% (119/121, and 76.7% (46/60, respectively, demonstrating that histological PCR had significantly higher accuracy (91.2% [165/181] than histological acid-fast staining (71.8% [130/181], P < 0.001. Parallel testing of histological AFB staining and PCR showed the

  10. Short Review

    DEFF Research Database (Denmark)

    Lynnerup, Niels; Rühli, Frank

    2015-01-01

    modality in ancient mummy research. The aim of this short review is to address the advantages and pitfalls of this particular technique for such unique samples. We recommend that when results of X-ray examination of mummies are presented, the specific recording data should be listed, and any given finds...

  11. Short fusion

    CERN Multimedia

    2002-01-01

    French and UK researchers are perfecting a particle accelerator technique that could aid the quest for fusion energy or make X-rays that are safer and produce higher-resolution images. Led by Dr Victor Malka from the Ecole Nationale Superieure des Techniques Avancees in Paris, the team has developed a better way of accelerating electrons over short distances (1 page).

  12. Short communication

    African Journals Online (AJOL)

    UPuser

    Short communication. Polymorphisms of the CAST gene in the Meishan and five other pig populations in China. Q.S. Wang. 1. , Y.C. Pan. 1#. , L.B. Sun. 2 and H. Meng. 1. 1 Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai. 201101, P.R. China. 2 Shanghai Institute of ...

  13. SHORT COMMUNICATION

    African Journals Online (AJOL)

    a

    ______. *Corresponding author. E-mail: vani_chem@yahoo.com. SHORT COMMUNICATION. OXIDATION OF L-CYSTINE BY CHROMIUM(VI) - A KINETIC STUDY. Kalyan Kumar Adari, Annapurna Nowduri and Vani Parvataneni*. Department of Inorganic and Analytical Chemistry, School of Chemistry, Andhra University,.

  14. Short communication

    NARCIS (Netherlands)

    Pantophlet, Andre J.; Gilbert, M.S.; Gerrits, W.J.J.; Vonk, R.J.

    2017-01-01

    Heavy veal calves (4-6 mo old) often develop problems with insulin sensitivity. This could lead to metabolic disorders and impaired animal growth performance. Studies in various animal species have shown that the supplementation of short-chain fructo-oligosaccharides (scFOS) can improve insulin

  15. Development of a dynamic short-term test method for installed thermal solar systems; Entwicklung eines dynamischen Kurzzeittestverfahrens fuer installierte thermische Solaranlagen

    Energy Technology Data Exchange (ETDEWEB)

    Beikircher, T.; Gut, M.; Kronthaler, P.; Oberdorf, C.; Schoelkopf, W. [Bayerisches Zentrum fuer Angewandte Energieforschung, Muenchen (Germany). Abt. Solarthermie und Biomasse

    1998-12-31

    A short-term test method for in-situ measurement of the collector field, pipelines and heat exchanger of large-surface solar systems was developed at ZAE Bayern, together with the necessary technical systems (mobile acquisition of meteorological data via telemetering, non-invasive surface temperature sensors and ultrasonic volume flow measuring instruments). Dynamic measurements were made for 11 days in a large-surface solar system of the ``Solarthermie 2000`` programme using the new measuring system. In order to optimize the evaluation procedure, the plant was simulated, and the influence of different models and operating conditions during the measurements on the prediction quality was investigated in detail. On this basis, it was possible to predict the long-term collector yield of the ZfS Hilden, which was measured for a period of 7 months, with an error of less than 5%. The method will be validated in two further industrial-scale systems. [Deutsch] Am ZAE Bayern wurde ein Kurzzeittestverfahren zur insitu-Vermessung des Kollektorkreises (Kollektorfeld, Rohrleitungen, Waermetauscher) grosser Solaranlagen entwickelt. Hierzu wurde eine der Aufgabenstellung angepasste Messtechnik entwickelt (Mobile meteorologische Datenerfassung mit Funkbetrieb, nicht-invasive Oberflaechen-Temperaturfuehler und Ultraschall-Volumenstrommessgeraete). Der Kollektorkreis einer grossen Solaranlage aus dem Programm Solarthermie 2000 wurde dynamisch ueber 11 Tage (29.10.-8.11.1997) mit der neuen Messtechnik vermessen. Zur Entwicklung eines geeigneten Auswerteverfahrens wurde die Anlage simulatorisch abgebildet und der Einfluss verschiedener Modellansaetze und der Betriebsbedingungen waehrend des Mess- und Vorhersagezeitraums auf die Vorhersageguete im Detail untersucht. Mit dem entwickelten Verfahren konnte aus der dynamischen Kurzzeitvermessung der in einer Langzeitmessung der ZfS Hilden ueber 7 Monate ermittelte Kollektorertrag nach dem solaren Waermetauscher auf deutlich besser als 5

  16. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  17. Analysis of the overdispersed clock in the short-term evolution of hepatitis C virus: Using the E1/E2 gene sequences to infer infection dates in a single source outbreak.

    Science.gov (United States)

    Wróbel, Borys; Torres-Puente, Manuela; Jiménez, Nuria; Bracho, María Alma; García-Robles, Inmaculada; Moya, Andrés; González-Candelas, Fernando

    2006-06-01

    The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such method, based on site stripping for clock detection, was proposed to unravel the clocklike molecular evolution in sequences showing high variability of evolutionary rates and in the presence of positive selection. Other alternatives imply accommodating heterogeneity in evolutionary rates at various levels, without eliminating any information from the data. Here we present the analysis of a data set of hepatitis C virus (HCV) sequences from 24 patients infected by a single individual with known dates of infection. We first used a simple criterion of relative substitution rate for site removal prior to a regression analysis. Time was regressed on maximum likelihood pairwise evolutionary distances between the sequences sampled from the source individual and infected patients. We show that it is indeed the fastest evolving sites that disturb the molecular clock and that these sites correspond to positively selected codons. The high computational efficiency of the regression analysis allowed us to compare the site-stripping scheme with random removal of sites. We demonstrate that removing the fast-evolving sites significantly increases the accuracy of estimation of infection times based on a single substitution rate. However, the time-of-infection estimations improved substantially when a more sophisticated and computationally demanding Bayesian method was used. This method was used with the same data set but keeping all the sequence positions in the analysis. Consequently, despite the distortion introduced by positive selection on evolutionary rates, it is possible to obtain quite accurate estimates of infection dates, a result of especial relevance for

  18. Short Communication

    African Journals Online (AJOL)

    huis

    Short Communication. QTL analysis of production traits on SSC3 in a Large White×Meishan pig resource family. B. Zuo. 1. , Y.Z. Xiong. 1#. , Y.H. Su. 2. , C.Y. Deng. 1. , M.G. Lei. 1. , F.E. Li. 1. , R. Zheng. 1 and S.W. Jiang. 1. 1 Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & Key Lab of Agricultural ...

  19. [Sequencing and analysis of the resistome of Streptomyces fradiae ATCC19609 in order to develop a test system for screening of new antimicrobial agents].

    Science.gov (United States)

    Vatlin, A A; Bekker, O B; Lysenkova, L N; Korolev, A M; Shchekotikhin, A E; Danilenko, V N

    2016-06-01

    The paper provides the annotation and data on sequencing the antibiotic resistance genes in Streptomyces fradiae strain ATCC19609, highly sensitive to different antibiotics. Genome analysis revealed four groups of genes that determined the resistome of the tested strain. These included classical antibiotic resistance genes (nine aminoglycoside phosphotransferase genes, two beta-lactamase genes, and the genes of puromycin N-acetyltransferase, phosphinothricin N-acetyltransferase, and aminoglycoside acetyltransferase); the genes of ATP-dependent ABC transporters, involved in the efflux of antibiotics from the cell (MacB-2, BcrA, two-subunit MDR1); the genes of positive and negative regulation of transcription (whiB and padR families); and the genes of post-translational modification (serine-threonine protein kinases). A comparative characteristic of aminoglycoside phosphotransferase genes in S. fradiae ATCC19609, S. lividans TK24, and S. albus J1074, the causative agent of actinomycosis, is provided. The possibility of using the S. fradiae strain ATCC19609 as the test system for selection of the macrolide antibiotic oligomycin A derivatives with different levels of activity is demonstrated. Analysis of more than 20 semisynthetic oligomycin A derivatives made it possible to divide them into three groups according to the level of activity: inactive (>1 nmol/disk), 10 substances; with medium activity level (0.05–1 nmol/disk), 12 substances; and more active (0.01–0.05 nmol/disk), 2 substances. Important for the activity of semisynthetic derivatives is the change in the position of the 33rd carbon atom in the oligomycin A molecule.

  20. Development of a new miniature short-residence-time annular centrifugal solvent extraction contactor for tests of process flowsheets in hot cells

    International Nuclear Information System (INIS)

    Lanoe, J.Y.; Rivalier, P.

    2000-01-01

    Researches undertaken on new nuclear fuel reprocessing extraction processes need tests of process flowsheets in hot cells. To this goal, a new miniature short residence-time annular centrifugal solvent extraction contactor was conceived and developed at Marcoule. This single stage contactor is composed of an outer stationary cylinder (made of transparent plexiglas on prototype and of stainless steel on models for hot cells) and a suspended inner rotating cylinder of stainless steel; the inside diameter of the rotor is 12 mm. Aqueous and organic phases are fed into the gap between the two cylinders. The mixture flows down the annular space and then up through an orifice at the bottom of the rotor. Into the rotor, the emulsion breaks rapidly under the centrifugal force (up to 600 g with rotor speed of 10,000 rpm). The separated phases flow over their weirs and discharge at the top in their collector rings. The liquid hold-up of this centrifugal contactor is approximately 6 mL. The use in hots cells needed original designs for: - the assembly of a single-stage contactor: every part (motor, rotor, stationary housing) is simply inserted on the other one without screws and nuts; - the assembly of multistage group: every stage is stacking in two rails and an intermediate part (supported on the two rails) links exit ports and their corresponding inlet ports. All the parts are pressed and sealed against a terminal plate with a screw. Separating capacity tests with. a prototype were conducted using water as the aqueous phase and hydrogenated tetra-propylene (TPH) as the organic phase with aqueous to organic (A/O) flow ratio equal to 1. The best performances were obtained with rotor speed ranging from 4000 to 5000 rpm; the total throughput was then up to 2 L.h -1 . For a total throughput of 300 mL.h -1 , the hold-up in the annular mixing zone varied from 0.5 to 1.5 mL according to the A/O ratio and the starting mode. A number of tests were also performed to measure the

  1. The novel as short story

    Directory of Open Access Journals (Sweden)

    Kirk Schlueter

    2013-06-01

    Full Text Available In recent history, the novel has been thought of and defined primarily as a long prose narrative. However, this has not been the case historically, as the original meaning of "novel" was for "a piece of news" or "a short story or novella." Returning to this original definition, I propose a new way of viewing the work known contemporarily as the novel as a collection, or sequence, of united short stories rather than a single indivisible work, with the component short stories or novellas comprising the sequence renamed as "novels." A brief examination of several classic works traditionally considered novels serves to illustrate how this change in definition will affect reading.

  2. Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

    Science.gov (United States)

    Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

    2003-01-01

    An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable

  3. The short-circuit test results of 6.9 kV/2.3 kV 400 kVA-class YBCO model transformer with fault current limiting function

    International Nuclear Information System (INIS)

    Tomioka, A.; Bohno, T.; Kakami, S.; Isozaki, M.; Watanabe, K.; Toyama, K.; Sugiyama, S.; Konno, M.; Gosho, Y.; Okamoto, H.; Hayashi, H.; Tsutsumi, T.; Iwakuma, M.; Saito, T.; Tanabe, K.; Shiohara, Y.

    2013-01-01

    Highlights: ► We manufactured the 400 kV A-class YBCO model transformer with FCL function. ► Short-circuit test was performed by applying 6.9 kV on primary side. ► The short-circuit current was limited to 174 A for a prospective current of 559 A. ► It agreed with the design and we also confirmed the I c did not degrade. ► The results suggest the possibility to design YBCO transformers with FCL function. -- Abstract: We are developing an elemental technology for 66/6.9 kV 20 MVA-class superconducting power transformer with fault current limiting function. In order to obtain the characteristics of YBCO conductor when the AC over current supplied to the conductor, the model coils were manufactured with YBCO tapes and tested. Based on these results, we manufactured the 6.9 kV/2.3 kV 400 kVA-class YBCO model transformer with fault current limiting function and performed short-circuit test. At the 0.25 s after short-circuit, the short-circuit current of primary winding was limited to about 174 A for a prospective current of 559 A. It was consistent with the design. The I–V characteristics of the winding did not change before and after the test. We consider the model transformer to be able to withstand AC over-current with the function of current limiting. The results suggest the possibility to design YBCO superconducting transformers with fault current limiting function for practical power grid

  4. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  5. Reducing Short-Wavelength Blue Light in Dry Eye Patients with Unstable Tear Film Improves Performance on Tests of Visual Acuity.

    Science.gov (United States)

    Kaido, Minako; Toda, Ikuko; Oobayashi, Tomoo; Kawashima, Motoko; Katada, Yusaku; Tsubota, Kazuo

    2016-01-01

    To investigate whether suppression of blue light can improve visual function in patients with short tear break up time (BUT) dry eye (DE). Twenty-two patients with short BUT DE (10 men, 12 women; mean age, 32.4 ± 6.4 years; age range, 23-43 years) and 18 healthy controls (10 men, 8 women; mean age, 30.1 ± 7.4 years; age range, 20-49 years) underwent functional visual acuity (VA) examinations with and without wearing eyeglasses with 50% blue light blocked lenses. The functional VA parameters were starting VA, functional VA, and visual maintenance ratio. The baseline mean values (logarithm of the minimum angle of resolution, logMAR) of functional VA and the visual maintenance ratio were significantly worse in the DE patients than in the controls (P 0.05). The DE patients had significant improvement in mean functional VA and visual maintenance ratio while wearing the glasses (P 0.05). Protecting the eyes from short-wavelength blue light may help to ameliorate visual impairment associated with tear instability in patients with DE. This finding represents a new concept, which is that the blue light exposure might be harmful to visual function in patients with short BUT DE.

  6. Reducing Short-Wavelength Blue Light in Dry Eye Patients with Unstable Tear Film Improves Performance on Tests of Visual Acuity.

    Directory of Open Access Journals (Sweden)

    Minako Kaido

    Full Text Available To investigate whether suppression of blue light can improve visual function in patients with short tear break up time (BUT dry eye (DE.Twenty-two patients with short BUT DE (10 men, 12 women; mean age, 32.4 ± 6.4 years; age range, 23-43 years and 18 healthy controls (10 men, 8 women; mean age, 30.1 ± 7.4 years; age range, 20-49 years underwent functional visual acuity (VA examinations with and without wearing eyeglasses with 50% blue light blocked lenses. The functional VA parameters were starting VA, functional VA, and visual maintenance ratio.The baseline mean values (logarithm of the minimum angle of resolution, logMAR of functional VA and the visual maintenance ratio were significantly worse in the DE patients than in the controls (P 0.05. The DE patients had significant improvement in mean functional VA and visual maintenance ratio while wearing the glasses (P 0.05.Protecting the eyes from short-wavelength blue light may help to ameliorate visual impairment associated with tear instability in patients with DE. This finding represents a new concept, which is that the blue light exposure might be harmful to visual function in patients with short BUT DE.

  7. Development and tests of short versions of the Youth Psychopathic traits Inventory and the Youth Psychopathic traits Inventory-Child Version

    NARCIS (Netherlands)

    van Baardewijk, Y.; Andershed, H.; Stegge, G.T.M.; Nilsson, K.W.; Scholte, E.; Vermeiren, R.R.J.M.

    2010-01-01

    The adolescent Youth Psychopathic Traits Inventory (YPI) and its child version (YPI-CV) are sound but lengthy instruments for measuring psychopathic traits in youths. The current study develops psychometrically strong short versions of these instruments. Samples used for item reduction were

  8. Test

    DEFF Research Database (Denmark)

    Bendixen, Carsten

    2014-01-01

    Bidrag med en kortfattet, introducerende, perspektiverende og begrebsafklarende fremstilling af begrebet test i det pædagogiske univers.......Bidrag med en kortfattet, introducerende, perspektiverende og begrebsafklarende fremstilling af begrebet test i det pædagogiske univers....

  9. The effect of short-term cortisol changes on growth hormone responses to the pyridostigmine-growth-hormone-releasing-hormone test in healthy adults and patients with suspected growth hormone deficiency

    DEFF Research Database (Denmark)

    Andersen, M; Støving, R K; Hangaard, J

    1998-01-01

    BACKGROUND AND AIMS: The interaction between cortisol and growth hormone (GH)-levels may significantly influence GH-responses to a stimulation test. In order to systematically analyse the interaction in a paired design, it is necessary to use a test, which has been proven safe and reliable...... such as the pyridostigmine-growth-hormone-releasing-hormone (PD-GHRH) test. Three groups of subjects with a different GH-secretory capacity were included. STUDY A: Eight healthy adults were tested seven times, once with placebo throughout the examination and six times with the PD-GHRH test following no glucocorticoid......-responses to a PD-GHRH test were reduced in all individuals during acute stress-appropriate cortisol levels and the percentage reduction in GH-levels was independent of the GH-secretory capacity. Clinically, we found that peak GH-responses were not significantly affected by a short break in conventional HC therapy...

  10. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

    International Nuclear Information System (INIS)

    Sanabria, Carlos; Lee, Peter J; Starch, William; Larbalestier, David C; Devred, Arnaud

    2015-01-01

    Prototype cable-in-conduit-conductors (CICCs) destined for use in the toroidal field and central solenoid coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3%–7% void fraction increase on the low pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb 3 Sn filament fractures observed in the longer twist pitch conductors. We report here a detailed strand-to-cable analysis of short and longer ‘baseline’ twist pitch CICCs. It was found that the use of internal tin (IT) strands in the longer ‘baseline’ twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of bronze process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the IT strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Conversely, the short twist pitch CICC made from bronze process strands preserved diffusion barrier integrity. (paper)

  11. Psychometric testing of the short version of the world health organization quality of life (WHOQOL-BREF questionnaire among pulmonary tuberculosis patients in Taiwan

    Directory of Open Access Journals (Sweden)

    Chung Wei-Sheng

    2012-08-01

    Full Text Available Abstract Background Studies on the effects of tuberculosis on a patient’s quality of life (QOL are scant. The objective of this study was to evaluate the psychometric properties of the Taiwan short version of the World Health Organization Quality of Life (WHOQOL-BREF questionnaire using patients with tuberculosis in Taiwan and healthy referents. Methods The Taiwanese short version of the WHOQOL-BREF was administered to patients with tuberculosis undergoing treatment and healthy referents from March 2007 to July 2007. Patients with tuberculosis (n = 140 and healthy referents (n = 130, matched by age, sex, and ethnicity, agreed to an interview. All participants lived in eastern Taiwan. Reliability assessments included internal consistency, whereas validity assessments included construct validity, convergent validity, and discriminant validity. Results More than half of these patients and referents were men (70.7% and 66.2%, respectively, and their average ages were 50.1 and 47.9 years, respectively. Approximately 60% of patients and referents were aboriginal Taiwanese (60.7% and 61.1%, respectively. The proportion with low socioeconomic status was greater for these patients. The internal consistency reliability coefficients were .92 and .93 for the patients and healthy referents, respectively. Exploratory factor analysis on the healthy referents displayed a 4-domain model, which was compatible with the original WHOQOL-BREF 4-domain model. However, for the TB patient group, after deleting 3 items, both exploratory and confirmatory factor analysis revealed a 6-domain model. Conclusion Psychometric evaluation of the Taiwan short version of the WHOQOL-BREF indicates that it has adequate reliability for use in research with TB patients in Taiwan. However, the factor structure generated from this TB patient sample differed from the WHO’s original 4-factor model, which raised a validity concern to apply the Taiwan short version of the WHOQOL

  12. Study on Oscillations during Short Circuit of MW-Scale IGBT Power Modules by Means of a 6-kA/1.1-kV Nondestructive Testing System

    DEFF Research Database (Denmark)

    Wu, Rui; Diaz Reigosa, Paula; Iannuzzo, Francesco

    2015-01-01

    This paper uses a 6-kA/1.1-kV nondestructive testing system for the analysis of the short-circuit behavior of insulated-gate bipolar transistor (IGBT) power modules. A field-programmable gate array enables the definition of control signals to an accuracy of 10 ns. Multiple 1.7-kV/1-kA IGBT power...... modules displayed severe divergent oscillations, which were subsequently characterized. Experimental tests indicate that nonnegligible circuit stray inductance plays an important role in the divergent oscillations. In addition, the temperature dependence of the transconductance is proposed as an important...

  13. Transcranial focal electrical stimulation via tripolar concentric ring electrodes does not modify the short- and long-term memory formation in rats evaluated in the novel object recognition test.

    Science.gov (United States)

    Rogel-Salazar, G; Luna-Munguía, H; Stevens, K E; Besio, W G

    2013-04-01

    Noninvasive transcranial focal electrical stimulation (TFS) via tripolar concentric ring electrodes (TCREs) has been under development as an alternative/complementary therapy for seizure control. Transcranial focal electrical stimulation has shown efficacy in attenuating penicillin-, pilocarpine-, and pentylenetetrazole-induced acute seizures in rat models. This study evaluated the effects of TFS via TCREs on the memory formation of healthy rats as a safety test of TFS. Short- and long-term memory formation was tested after the application of TFS using the novel object recognition (NOR) test. The following independent groups were used: naïve, control (without TFS), and TFS (treated). The naïve, control, and stimulated groups spent more time investigating the new object than the familiar one during the test phase. Transcranial focal electrical stimulation via TCREs given once does not modify the short- and long-term memory formation in rats in the NOR test. Results provide an important step towards a better understanding for the safe usage of TFS via TCREs. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Comparison of Short and Long Versions of the Prudhoe Cognitive Function Test and the K-BIT in Participants with Intellectual Impairment

    Science.gov (United States)

    Tyrer, Stephen P.; Wigham, Ann; Cicchetti, Domenic; Margallo-Lana, Marisa; Moore, P. Brian; Reid, Barbara E.

    2010-01-01

    The Prudhoe Cognitive Function Test (PCFT) directly measures the cognitive abilities of people with intellectual impairment. This study examined the relationship between this instrument and the Kaufman Brief Intelligence Test (K-BIT) and two shorter versions of the same scale. High correlations between the verbal and performance sections of the…

  15. Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.

    KAUST Repository

    Sayadi, Ahmed; Briganti, Leonardo; Tramontano, Anna; Via, Allegra

    2011-01-01

    The function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length

  16. Translation, cultural adaptation assessment, and both validity and reliability testing of the kidney disease quality of life - short form version 1.3 for use with Iranian patients

    DEFF Research Database (Denmark)

    Pakpour, Amir; Yekaninejad, Mirsaeed; Mølsted, Stig

    2011-01-01

    AIM: The aims of the study were to translate the Kidney Disease Quality of Life--Short Form version 1.3 (KDQOL-SF ver. 1.3) questionnaire into Iranian (Farsi), and to then assess it in terms of validity and reliability on Iranian patients. METHODS: The questionnaire was first translated into Farsi...... a larger group (212 patients with end-stage renal disease on haemodialysis). Afterwards, reliability was estimated by internal consistency, and validity was assessed using known group comparisons and constructs for the patient group as a whole. Finally, the factor structure of the questionnaire...... be summarized into an 11 factor structure that jointly accounted for 79.81% of the variance. CONCLUSION: The Iranian version of the KDQOL-SF questionnaire is both highly reliable and valid for use with Iranian patients on haemodialysis....

  17. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  18. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  19. Rapid, automated, nonradiometric susceptibility testing of Mycobacterium tuberculosis complex to four first-line antituberculous drugs used in standard short-course chemotherapy

    DEFF Research Database (Denmark)

    Johansen, Isik Somuncu; Thomsen, Vibeke Østergaard; Marjamäki, Merja

    2004-01-01

    The increasing prevalence of drug-resistant tuberculosis necessitates rapid and accurate susceptibility testing. The nonradiometric BACTEC Mycobacteria Growth Indicator Tube 960 (MGIT) system for susceptibility testing was evaluated on 222 clinical Mycobacterium tuberculosis complex isolates...... for isoniazid, rifampin, and ethambutol. Fifty-seven of the isolates were tested for pyrazinamide. Results were compared to those of radiometric BACTEC 460 system and discrepancies were resolved by the agar proportion method. We found an overall agreement of 99.0% for isoniazid, 99.5% for rifampin, 98.......2% for ethambutol, and 100% for pyrazinamide. After resolution of discrepancies, MGIT yielded no false susceptibility for rifampin and isoniazid. Although turnaround times were comparable, MGIT provides an advantage as inoculation can be done on any weekday as the growth is monitored automatically. The automated...

  20. The palatability of corn oil and linoleic acid to mice as measured by short-term two-bottle choice and licking tests.

    Science.gov (United States)

    Yoneda, Takeshi; Saitou, Katsuyoshi; Mizushige, Takafumi; Matsumura, Shigenobu; Manabe, Yasuko; Tsuzuki, Satoshi; Inoue, Kazuo; Fushiki, Tohru

    2007-06-08

    Free fatty acids (FFAs) were reported to be recognized in the oral cavity and possibly involved in fatty foods recognition. To understand the importance of oil recognition in the oral cavity, we investigated the effect of various concentrations of a fatty acid or corn oil on fluid intake as well as mice's preferences in a two-bottle choice test and a licking test. Linoleic acid (LA), which is a main component of corn oil, was used as a representative FFA. In the two-bottle choice test between a pair of different concentrations of corn oil, the mice consistently adopted the higher concentration of corn oil. In the licking test for corn oil, the licking rates for the serial concentration of corn oils (0, 1, 5, 10 and 100%) were increased in a concentration-dependent manner. On the other hand, in the two-bottle test for a pair of different concentrations of LA (0, 0.125, 0.25 and 1%), 0.25% and 1% LA were preferred to mineral oil, but 0.25% and 1% LA were preferred equally in mice. In the licking test for LA, the mice showed the largest number of initial lickings for the 1% LA, while the licking rates for the high concentration of LA decreased. These results suggest that mice could discriminate the concentration of corn oil and LA in the oral cavity. We also suggest that pure corn oil is a highly preferable solution, while an optimal concentration of LA according to the preferences of mice is a low-range concentration (0.25-1%).